• 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 : unliganded (2) / substrates (2) / FDA drugs (18)

1 G 6 L				Z-Score 35.0  RMSD 0.4A  (CACB, TETHERED DIMER) Ligand  None Mu(L)  V                                 S                                                         M    Mu(R)  V                                 S                                                            DifL                              +                                                                     DifR                              +                                                                     Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR0000R Ch R 30001R00R000000RRG00000R0QBGRG0000000000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--
1 L V 1				Z-Score 35.4  RMSD 0.4A  (CACB, TETHERED DIMER) Ligand  None Mu(L)  V                                 S                                                         M    Mu(R)  V                                 S                                                         A  DifL                              +                                                         + DifR       +                      +                                     +                   ++ Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RRG000000000R0R00000QBAAAABR0000O Ch R 30001RG0R000000RRG00000R0QBGRG0000000000000000000QB000000000R00000R0G000000000R0R00000QB1AAABR000--
3 D O X				Z-Score 36.0  RMSD 0.4A  (CACB, TETHERED DIMER) Ligand substrate MC-CA Mu(L)  V                                 S                                                         M    Mu(R)  V                                 S                                                         A  DifL                                                                     +                  ++ DifR       + Ch L --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RR0000000000R0R00000QB1AAABR0000O Ch R 30001RG0R000000RRG00000R0QBGR00000000000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--
3 D 3 T				Z-Score 34.2  RMSD 0.6A  (CACB) Ligand substrate P1-P6 Muta                    R    N         DI    K                           K                   M   L DifL       +                          +++ DifR     +                            +++ Ch L --001RG0R000000RRG00000R0QBGR00001RG00000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --00RR00R000000RRG00000R0QBGR00001RG0000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--
1 H X B				Z-Score 35.0  RMSD 0.4A  (CBCA) Ligand saquinavir (approved in 1995, the first PI) Muta   V                                 S DifL                              +                                                +     +   + DifR                                                  +                                     ++ Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RRG00000000000R00030QA9AAABR000-- Ch R --001R00R000000RRG00000R0QBGR000000000000000000000B000000000R00000RRG000000000R0R00000QB9AAABR000--
1 S G U				Z-Score 34.6  RMSD 0.5A  (CACB) Ligand indinavir (1996) Muta                    R           IF  IS                V        P       V          A V     M DifL                                                                     +         + DifR                                                   +                 +         +        ++ Ch L --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RR000000000000R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR00000000000000000000Q3000000000R00000RR000000000000R00000QB1AAABR000--
2 B 7 Z				Z-Score 34.7  RMSD 0.5A  (CACB) Ligand indinavir (1996) Muta                    R           IF  IS        I                P       V          A V     M DifL                                  +                                                     + DifR                                  +               ++                                    ++ Ch L --001R00R000000RRG00000R0QBGR0000R0000000000000000R000000000R00000RRG000000000R0R00000QBAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR0000R0000000000000000R000000000R00000RRG000000000R0R00000QB1AAABR000--
1 R L 8				Z-Score 35.8  RMSD 0.4A  (CACB) Ligand ritonavir (1996) Muta                                     S                                            A DifL       +                                                            +                   ++ DifR                                                                    + Ch L --001RG0R000000RRG00000R0QBGR000000000000000000000R000000000R00000R0G000000000R0R00000QB1AAABR000-- Ch R --001R00R000000RRG00000R0QBGR00000000000000000000QB000000000R00000R0G000000000R0R00000QAAAAABR000--
1 S H 9				Z-Score 33.9  RMSD 0.5A  (CACB) Ligand ritonavir (1996) Muta                    R           IF  IS                V        P       V          A V     M DifL       +                      +             +                                  + DifR       +                                                                       +        + Ch L --001RG0R000000RRG00000R0QBGRG00000000000003000000R000000000R00000RRG00000000000R00000QAAAAABR000-- Ch R --001RG0R000000RRG00000R0QBGR00000000000000000000QB000000000R00000RRG00000000000R00000QBAAAABR000--
2 B 6 0				Z-Score 34.7  RMSD 0.5A  (CBCA) Ligand ritonavir (1996) Muta                    R           IF  IS                         P       V          A       M DifL                              +                                      + DifR                                                                     +            +     ++ Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RR0000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR00000000000000000000QB000000000R00000RR0000000000R0RG0000QB1AAABR000--
2 P Y M				Z-Score 35.1  RMSD 0.5A  (CACB) Ligand nelfinavir (1997) Muta                              N      S                                                  D DifL                              +                                      + DifR                                                  ++ Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RR0000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000--
2 P Y N				Z-Score 35.3  RMSD 0.4A  (CBCA) Ligand nelfinavir (1997) Muta                              N      S                                 V DifL                                                                               + DifR                                                  ++                           + Ch L --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG00000000030R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG00000000030R00000QAAAAABR000--
2 Q 6 3				Z-Score 35.2  RMSD 0.5A  (CACB) Ligand nelfinavir (1997) Muta                              N      S                 A                                  M DifL                              + DifR                              +                   ++ Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000--
2 Q 6 4				Z-Score 35.6  RMSD 0.4A  (CBCA) Ligand nelfinavir (1997) Muta                              N      S DifL                              + DifR                              +                   ++ Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGRG0000000000000000000RG000000000R00000RRG000000000R0R00000QAAAAABR000--
2 Q A K				Z-Score 35.2  RMSD 0.5A  (CACB) Ligand nelfinavir (1997) Muta                              N      S                 A                                  M DifL                                                                     + DifR                              +                                                + Ch L --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RR0000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGRG0000000000000000000QB000000000R00000RRG00000000000R00000QAAAAABR000--
1 H P V				Z-Score 35.0  RMSD 0.4A  (CBCA) Ligand amprenavir (1999)  Ki=0.6nM Muta                                     S DifL     + DifR                        +                                          + Ch L --00PR00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG0000000QBGR00000000000000000000QB000000000R000000RG000000000R0R00000QAAAAABR000--
2 R K G				Z-Score 34.1  RMSD 0.5A  (CACB, length 100) Ligand lopinavir (2000) Muta          F  V  A   M           I  EE S     T  VV      M         V      V          A DifL                                   +++                                + DifR                                   +++             +                  + Ch L --001R00R000000RRG00000R0QBGR00000QBG00000000000000R000000000R00000RR0000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR00000QBG00000000000000B000000000R00000RR0000000000R0R00000QAAAAABR000--
2 R K F				Z-Score 34.9  RMSD 0.5A  (CBCA) Ligand lopinavir (2000)  Ki=0.83nM  (0.018nM for WT) Muta          F  V  A   M           I    S     T  VV      M         V      V          A DifL         + DifR       + +                                                           + Ch L --001R003000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001RG03000000RRG00000R0QBGR00000000000000000000QB000000000R00000RR0000000000R0R00000QAAAAABR000--
2 Z 5 4				Z-Score 35.7  RMSD 0.4A  (CACB) Ligand lopinavir (2000)  Ki=100-fold against the wild type Muta                                     S         A      V DifL                                                                     + DifR                                                                     + Ch L --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RR0000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGR00000000000000000000QB000000000R00000RR0000000000R0R00000QAAAAABR000--
1 M U I				Z-Score 34.5  RMSD 0.4A  (CACB) Ligand lopinavir (2000) Muta                                     S DifL                                        +         ++             +                      ++ DifR                        + Ch L --001R00R000000RRG00000R0QBGR0000000000G000000000QB000000000R00030RRG000000000R0R00000QB1AAABR000-- Ch R --001R00R000000RRG0000030QBGR00000000000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--
2 Q H C				Z-Score 35.5  RMSD 0.4A  (CACB) Ligand lopinavir (2000) Muta                                     S         A DifL DifR       + Ch L --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001RG0R000000RRG00000R0QBGR00000000000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--
2 A Q U				Z-Score 35.7  RMSD 0.4A  (CACB) Ligand atazanavir (2003)  Ki=0.48nM Muta                                     S DifL                              +                    + DifR                              + Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000B000000000R00000RRG000000000R0R00000QAAAAABR000-- Ch R --001R00R000000RRG00000R0QBGRG0000000000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--

[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