• Backbone structures are obtained using ProteinViewer, where N-terminal is colored red and C-terminal blue.
• Superposition of molecules and their Z-scores and RMSDs are computed by the DaliLite server.
  
• Click the images to view larger image.
• See the bottom for brief explanation of the D² codes. 

	Superposition of the current dimer and the dimer of 2NPH		Superposition of chains	D2 code sequences
P D B I D	(Front view) Cur.: yellow 2NPH: blue	(Top view) Cur.: yellow 2NPH: blue	(Front view) Chain A: black Chain B: white	Z-score and RMSD of the dimer superposition with 2NPH (CACB or CBCA1)) Ligand name (value of the inhibitor constant Ki) Mutations from the Consensus B amino acid sequence2) (Red are resistance mutations) Difference with 2NPH (chain L) Difference with 2NPH (chain R) D2 code of chain L (left in the front view) D2 code of chain R (right in the front view)

The base D² code sequences for the dimer comparisons (2NPH: wild type HIV-1 PR complexed with the substrate RT-RH)

2 N P H

Z-Score -  RMSD 0.0A (identical)  (CACB) Ligand substrate RT-RH (colored black in the left figures)                1         2         3         4         5         6         7         8         9      123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 Muta   V                                 S                                                         M    DifL DifR Ch L --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR00000000000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--

Crystal structures : peptidomimetics (31)

1 B D Q				Z-Score 33.7  RMSD 0.6A  (CBCA) Ligand IM1(SB203386)  Ki=18nM Muta                               SIVAGIE         V                                  I DifL     +                        +                                                      + DifR     + +                      +    + +        +   ++                         +       + Ch L --00RR00R000000RRG00000R0QBGRG00000000000000000000R000000000R000R0RRG000000000R0R00030QAAAAABR000-- Ch R --00QRG0R000000RRG00000R0QBGRG0000R0R0000000030001R000000000R00000RRG000000030R0R000R0QAAAAABR000--
1 B D L				Z-Score 32.6  RMSD 0.7A  (CACB) Ligand IM1(SB203386) Muta                               SIVAGIE DifL     + + +              +     +    +                +                                + DifR     + +                      +    +              ++      +  +                       +        + Ch L --00PRG00000000RRG0000000QBGRG0000R000000000000000RG00000000R00000RRG000000000R0R000R0QAAAAABR000-- Ch R --00QRG0R000000RRG00000R0QBGRG0000R000000000000000R000000R00000000RRG000000000R0R000R0QAAAAAB0000--
1 B D R				Z-Score 34.1  RMSD 0.6A  (CACB) Ligand IM1(SB203386) Muta                               SVVAGIE DifL     +                             + DifR                              +    +              ++                                 + Ch L --00RR00R000000RRG00000R0QBGR00000O000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGRG0000O000000000000000R000000000R00000RRG000000000R0R00030QAAAAABR000--
1 S B G				Z-Score 34.9  RMSD 0.4A  (CBCA) Ligand IM1(SB203386)  Ki=18nM Muta   DifL                              +                                  +  +          +        + DifR     +          +       +     + Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000R000000000R000R0ROG00000000000R00000QBAAAABR000-- Ch R --00RR00R0000000RG0000030QBGRG0000000000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--
1 A X A				Z-Score 34.9  RMSD 0.4A  (CACB) Ligand U0E(U-89360E) Muta                            S        S DifL     +                  +     +                                                + DifR     +                  +     +      +            ++                                   + Ch L --00PR00R000000RRG0000000QBGRG00000000000000000000R000000000R00000RRG00000000000R00000QAAAAABR000-- Ch R --00PR00R000000RRG0000000QBGRG000000300000000000020000000000R00000RRG000000000R0R00000PAAAAABR000--
1 G N M				Z-Score 35.1  RMSD 0.4A  (CBCA) Ligand U0E(U-89360E) Mu(L)                                    S                                            D Mu(R)                                    S                                            N DifL                              +                    +                                 + DifR                        +                                                      +        + Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000B000000000R00000RRG000000000R0R000R0QAAAAABR000-- Ch R --001R00R000000RRG0000000QBGR00000000000000000000QB000000000R00000RRG00000000000R00000QBAAAABR000--
1 G N N				Z-Score 35.2  RMSD 0.4A  (CBCA) Ligand U0E(U-89360E) Muta                                     S                                            N DifL                        +     + DifR       +                +                         ++                           +        + Ch L --001R00R000000RRG0000030QBGRG00000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001RG0R000000RRG0000000QBGR000000000000000000000R000000000R00000RRG00000000000R00000QBAAAABR000--
1 G N O				Z-Score 35.2  RMSD 0.4A  (CACB) Ligand U0E(U-89360E) Muta                                     S DifL     +                                                               +         + DifR       +                + Ch L --00PR00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RR0000000000O0R00000QAAAAABR000-- Ch R --001RG0R000000RRG0000000QBGR00000000000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--
1 H B V				Z-Score 34.7  RMSD 0.4A  (CBCA) Ligand GAN(SB203238)  Ki=430nM Muta                                     S DifL       +                      +                                                               + DifR                        +     +                                                          + Ch L --001RG0R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RRG000000000R0R00000QAAAAAB3000-- Ch R --001R00R000000RRG0000030QBGRG0000000000000000000QB000000000R00000RRG000000000R0R000R0QA2AAABR000--
1 H P S				Z-Score 35.0  RMSD 0.4A  (CBCA) Ligand RUN(SB206343)  Ki=0.6nM Muta                                     S DifL       +                      +                                  + DifR                        +          + + Ch L --001RG0R000000RRG00000R0QBGRG00000000000000000000R000000000R000O0RRG000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG0000000QBGR00000R0R000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--
1 I Z I				Z-Score 35.4  RMSD 0.4A  (CACB) Ligand Q50(QF34)  (potent against multi-drug resistant PR variants) Muta                                                                       V          T V DifL     +                        +                                      +         +        + DifR                              +                    +                 +                  + Ch L --00PR00R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RR0000000000O0R00000QBAAAABR000-- Ch R --001R00R000000RRG00000R0QBGRG0000000000000000000Q0000000000R00000RR0000000000R0R00000QBAAAABR000--
1 M 0 B				Z-Score 35.6  RMSD 0.4A  (CBCA) Ligand Peptide(OE)  Ki=1.53nM Muta                                     S DifL       +                      + DifR       +                      + Ch L --001RG0R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001RG0R000000RRG00000R0QBGRG0000000000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--
1 L Z Q				Z-Score 35.5  RMSD 0.4A  (CBCA) Ligand Peptide(OE)  Ki=4.1nM Muta                                     S                                 V          T V DifL                              +                    +                 + DifR                              +      +             +                 + Ch L --001R00R000000RRG00000R0QBGRG000000000000000000000000000000R00000RR0000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGRG000000R000000000000Q0000000000R00000RR0000000000R0R00000QAAAAABR000--
1 A 8 G				Z-Score 34.7  RMSD 0.5A  (CACB) Ligand Peptide(SDZ283-910) Muta  DifL                        +     +                    +         +   +                      + DifR                              +                   +                                     + Ch L --001R00R000000RRG0000000QBGRG00000000000000000000R0000000003000R0RRG000000000R0R00000QBAAAABR000-- Ch R --001R00R000000RRG00000R0QBGRG00000000000000000000B000000000R00000RRG000000000R0R00000QBAAAABR000--
1 O D Y				Z-Score 35.0  RMSD 0.4A  (CACB) Ligand LP1(LP-130)  Ki=8nM Muta   V                                 S   A DifL                                                  ++ DifR                                                                               + Ch L --001R00R000000RRG00000R0QBGR00000000000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR00000000000000000000QB000000000R00000RRG00000000000R00000QAAAAABR000--
1 A A Q				Z-Score 33.5  RMSD 0.6A  (CACB) Ligand PSI(Hydroxyethylene isostere inhibitors) Muta                                     S                         I DifL                        +     +                                                +     +        + DifR                              +                   ++                           +     +        + Ch L --001R00R000000RRG0000030QBGRG00000000000000000000R000000000R00000RRG00000000000R00030QAAAAAB0000-- Ch R --001R00R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RRG00000000000R00030QAAAAABO000--
1 U 8 G				Z-Score 35.5  RMSD 0.4A  (CACB) Ligand Peptide(phenylnorstatine inhibitor) Muta                                     S DifL                                                                                        ++ DifR                                                  ++                                    ++ Ch L --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QB1AAABR000-- Ch R --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QB1AAABR000--
1 Z L F				Z-Score 35.1  RMSD 0.4A  (CBCA) Ligand Peptide(hydroxyethylamine inhibitor) Muta                                     S                                 V          T V DifL                        +     +                                      + DifR                        +     +                   +                  + Ch L --001R00R000000RRG0000000QBGRG00000000000000000000R000000000R00000RR0000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG0000030QBGRG00000000000000000001B000000000R00000RR0000000000R0R00000QAAAAABR000--
1 Z P K				Z-Score 35.1  RMSD 0.4A  (CBCA) Ligand Peptide(hydroxyethylamine inhibitor) Muta                                     S                             X   V          T V DifL                                                                     + DifR                                                   + Ch L --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RR0000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR00000000000000000000Q0000000000R00000RRG000000000R0R00000QAAAAABR000--
1 Z S F				Z-Score 35.0  RMSD 0.4A  (CBCA) Ligand peptide(hydroxyethylamine inhibitor, R-config) Muta                                     S                             X DifL                        +     +      + DifR                              + Ch L --001R00R000000RRG0000000QBGRG000000R0000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGRG0000000000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--
1 Z S R				Z-Score 35.4  RMSD 0.3A  (CACB) Ligand Peptide(hydroxyethylamine inhibitor, S-config) Muta                                     S                             X DifL                              +                    + DifR                              +                   + Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000B000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGRG00000000000000000000B000000000R00000RRG000000000R0R00000QAAAAABR000--
1 F Q X				Z-Score 34.8  RMSD 0.6A  (CACB) Ligand Peptide(hydroxyethylamine inhibitor) Muta                                     S DifL                              +                   ++                                    ++ DifR       +                      +                    +                                    ++ Ch L --001R00R000000RRG00000R0QBGRG0000000000000000000R0000000000R00000RRG000000000R0R00000QB1AAABR000-- Ch R --001RG0R000000RRG00000R0QBGRG0000000000000000000Q0000000000R00000RRG000000000R0R00000QB1AAABR000--
2 F L E				Z-Score 36.1  RMSD 0.4A  (CBCA) Ligand GOL(C44H64N8H8) Muta                                     S                                            A DifL                              +                                                         + DifR                              +                    +                                    + Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RRG000000000R0R00000QBAAAABR000-- Ch R --001R00R000000RRG00000R0QBGRG0000000000000000000Q0000000000R00000RRG000000000R0R00000QBAAAABR000--
2 P 3 A				Z-Score 34.7  RMSD 0.4A  (CBCA) Ligand 3TL(TL-3)  Ki=7-fold against 2P3B Muta       K                             A   K            V        P   X   V          A       M DifL                                                                     + DifR                                                  ++ Ch L --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RR0000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR0000000000000000000003000000000R00000RRG000000000R0R00000QAAAAABR000--
2 P 3 B				Z-Score 34.2  RMSD 0.5A  (CACB) Ligand 3TL(TL-3) Mu(L)      K                             S Mu(R)      K                             S                             X DifL  DifR                                                  ++                           + Ch L --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG00000000000R00000QAAAAABR000--
2 P 3 C				Z-Score 34.0  RMSD 0.6A  (CACB) Ligand 3TL(TL-3)  Ki=3-fold against 2P3B Muta       K       V                   DIA                   K  ENVSL  X                     M DifL                              +    + +                                            + DifR                              +    + +            ++                              + Ch L --001R00R000000RRG00000R0QBGRG0000R0O0000000000000R000000000R00000RRG000000000R0RG0000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGRG0000R0O0000000000000R000000000R00000RRG000000000R0RG0000QAAAAABR000--
2 P 3 D				Z-Score 34.2  RMSD 0.6A  (CACB) Ligand 3TL(TL-3)  Ki=54-fold against 2P3B Muta       K  I    VE   R              DI  S K    I    R  V  K  ED        R V A       A      M DifL     +                             +                                               + DifR     +                             +              ++ Ch L --00RR00R000000RRG00000R0QBGR00000R000000000000000R000000000R00000RRG000000000R0R0O000QAAAAABR000-- Ch R --00RR00R000000RRG00000R0QBGR00000R000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000--
1 H O S				Z-Score 34.5  RMSD 0.5A  (CACB) Ligand PHP(SB202144)  Ki=2.8nM  (C2 symmetry and pseudo-symmetry inhibitors) Muta                                     S DifL     +                  +     +      +                                                  + DifR                                                  ++             +             +     + Ch L --00RR00R000000RRG0000030QBGRG000000R0000000000000R000000000R00000RRG000000000R0R00000QBAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R000O0RRG00000000000R000R0QAAAAABR000--
1 O D X				Z-Score 34.4  RMSD 0.5A  (CBCA) Ligand HPH(BMS-182193)  (C2 symmetry and pseudo-symmetry inhibitors) Muta                                     S                                 T          A DifL     + + DifR                                     +             +                 +         +         + Ch L --003RG0R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR00000003000000000000Q0000000000R00000RR000000000000R00000QA2AAABR000--
1 V I J				Z-Score 33.5  RMSD 0.6A  (CBCA) Ligand BAY(HOE/BAY 793)  (C2 symmetry and pseudo-symmetry inhibitors) Muta  DifL     +                  +     +                    +        +        +         +        ++ DifR                        +            +                                                  ++  + Ch L --00RR00R000000RRG00000O0QBGRG000000000000000000000000000001R00000RR000000000000R00000QB1AAABR000-- Ch R --001R00R000000RRG0000000QBGR00000003000000000000QB000000000R00000RRG000000000R0R00000QB1ABHBR000--
9 H V P				Z-Score 34.2  RMSD 0.5A  (CBCA) Ligand COR(A-74704)  Ki=4.5nM  (C2 symmetry and pseudo-symmetry inhibitors) Muta  DifL                              +                              +   +             +     + DifR     +          +             +                                  +             +        + Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000R0000000000000R0RRG00000000030R000R0QAAAAABR000-- Ch R --00RR00R0000000RG00000R0QBGRG0000000000000000000QB000000000R000O0RRG00000000000R00000QBAAAABR000--

[The D² codes]

• 0 = DDDDD    (Extended strand, small blue spheres)
• 1 = DDDDU
• 2 = DDDUD
• 3 = DDDUU
• 8 = DUDDD
• 9 = DUDDU
• A = DUDUD    (Helix, large red spheres)
• B = DUDUU    (C-cap, large orange spheres)
• G = UDDDD    (Large green spheres)
• H = UDDDU
• I = UDDUD
• J = UDDUU
• O = UUDDD
• P = UUDDU
• Q = UUDUD    (N-cap, large orange spheres)
• R = UUDUU    (Turn, large yellow spheres)

[The DSSP code]

• H = alpha helix
• B = residue in isolated beta-bridge
• E = extended strand, participates in beta ladder
• G = 3-helix (3/10 helix)
• I = 5 helix (pi helix)
• T = hydrogen bonded turn
• S = bend
• L = no assigned structure