[HIV-1 PR variants complexed with non-peptide based inhibitors (P 61)]




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)

1) The CACB and CBCA flag
: CACB indicates that chain L and chain R correspond to chain A and chain B of the PDB file, respectively.
                                                    CBCA indicates that chain L and chain R correspond to chain B and chain A of the PDB file, respectively.

                                              1         2         3         4         5         6         7         8         9
                                     123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789
2) Consensus B amino acid sequence : PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF



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
jpg image jpg image
jpg image 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 : non-peptide based inhibitors (18)

1
H
T
F
jpg image jpg image
jpg image Z-Score 34.9  RMSD 0.4A  (CACB)
Ligand G26(GR126045)
Muta                                     S
DifL                        +     +
DifR       +                +                         +                                     ++    +
Ch L --001R00R000000RRG0000030QBGRG00000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000--
Ch R --001RG0R000000RRG0000030QBGR000000000000000000000B000000000R00000RRG000000000R0R00000QB1AAAB3000--
1
H
V
H
jpg image jpg image
jpg image Z-Score 34.0  RMSD 0.6A  (CBCA)
Ligand Q82(cyclic cyanoguanidine)
Muta   V                                 S                                                         A
DifL                        +                                                      +
DifR         +              +                         ++                 +
Ch L --001R00R000000RRG0000030QBGR000000000000000000000R000000000R00000RRG00000000000R00000QAAAAABR000--
Ch R --001R00O000000RRG0000030QBGR0000000000000000000030000000000R00000RR0000000000R0R00000QAAAAABR000--
1
B
V
7
jpg image jpg image
jpg image Z-Score 34.8  RMSD 0.4A  (CACB)
Ligand XV6(XV638)  Ki=8-fold against the wild type
Muta   V                                 S                                            F
DifL     +   +              +                                    +                 +
DifR                              +                                    +           +
Ch L --00PR000000000RRG0000000QBGR000000000000000000000R000000000O00000RRG00000000030R00000QAAAAABR000--
Ch R --001R00R000000RRG00000R0QBGRG0000000000000000000QB000000000R000000RG00000000000R00000QAAAAABR000--
1
B
V
9
jpg image jpg image
jpg image Z-Score 35.1  RMSD 0.4A  (CBCA)
Ligand XV6(XV638)  Ki=8-fold against the wild type
Muta   V                                 S                                              V
DifL                        +                                                      +
DifR     +                                            +                            +
Ch L --001R00R000000RRG0000030QBGR000000000000000000000R000000000R00000RRG00000000030R00000QAAAAABR000--
Ch R --00RR00R000000RRG00000R0QBGR000000000000000000000B000000000R00000RRG00000000000R00000QAAAAABR000--
1
B
W
A
jpg image jpg image
jpg image Z-Score 35.1  RMSD 0.4A  (CBCA)
Ligand XV6(XV638)  Ki=8-fold against the wild type
Muta   V                                 S                                            F
DifL     +   +              +                                          +           +
DifR                                                  +                  +
Ch L --00RR000000000RRG0000000QBGR000000000000000000000R000000000R00000ORG00000000000R00000QAAAAABR000--
Ch R --001R00R000000RRG00000R0QBGR000000000000000000000B000000000R00000RR0000000000R0R00000QAAAAABR000--
1
Q
B
R
jpg image jpg image
jpg image Z-Score 34.8  RMSD 0.5A  (CACB)
Ligand XV6(XV638)  Ki=0.03nM
Muta   V                                 S                                                         A
DifL     +                  +                                           +
DifR     +                  +                         ++        +                  +        ++    +
Ch L --00RR00R000000RRG0000000QBGR000000000000000000000R000000000R00000R0G000000000R0R00000QAAAAABR000--
Ch R --00RR00R000000RRG0000030QBGR000000000000000000001R000000001R00000RRG00000000000R00000QB1AAAB0000--
1
B
W
B
jpg image jpg image
jpg image Z-Score 35.0  RMSD 0.5A  (CBCA)
Ligand 146(SD146)  Ki=8-fold against the wild type
Muta   V                                 S                                            F
DifL     +
DifR                                                  ++               +           +
Ch L --00RR00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000--
Ch R --001R00R000000RRG00000R0QBGR0000000000000000000020000000000R00000ORG00000000000R00000QAAAAABR000--
1
Q
B
T
jpg image jpg image
jpg image Z-Score 34.9  RMSD 0.5A  (CACB)
Ligand 146(SD146)  Ki=0.02nM
Muta   V                                 S                                                         A
DifL     +   +
DifR                        +                         ++               +
Ch L --00QR000000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000--
Ch R --001R00R000000RRG0000000QBGR000000000000000000000R000000000R00000ORG000000000R0R00000QAAAAABR000--
1
Q
B
U
jpg image jpg image
jpg image Z-Score 34.6  RMSD 0.5A  (CACB)
Ligand 846
Muta   V                                 S                                                         A
DifL     +                  +                                                      +        +
DifR     +  +               +                          +
Ch L --00RR00R000000RRG0000030QBGR000000000000000000000R000000000R00000RRG00000000000R00000QBAAAABR000--
Ch R --00RR0OR000000RRG0000030QBGR000000000000000000000B000000000R00000RRG000000000R0R00000QAAAAABR000--
1
H
W
R
jpg image jpg image
jpg image Z-Score 34.7  RMSD 0.5A  (CACB)
Ligand 216(XK216)  Ki=4.70nM
Muta   V                                 S                                                         A
DifL                                       + +                        ++           +
DifR       + +              +                         +                  +         +
Ch L --001R00R000000RRG00000R0QBGR000000000R0R000000000R000000000R000030RG00000000000R00000QAAAAABR000--
Ch R --001RG0O000000RRG0000000QBGR000000000000000000000B000000000R00000RRO00000000000R00000QAAAAABR000--
1
H
V
R
jpg image jpg image
jpg image Z-Score 35.1  RMSD 0.4A  (CBCA)
Ligand XK2(XK263)  Ki=0.31nM
Muta   V                                 S                                                         A
DifL                        +                                                      +
DifR       +                +                         ++               +
Ch L --001R00R000000RRG0000030QBGR000000000000000000000R000000000R00000RRG00000000000R00000QAAAAABR000--
Ch R --001RG0R000000RRG00000O0QBGR00000000000000000000R0000000000R000000RG000000000R0R00000QAAAAABR000--
1
D
M
P
jpg image jpg image
jpg image Z-Score 34.0  RMSD 0.5A  (CBCA)
Ligand DMQ(DMP450)  Ki=0.34nM
Muta   V                                 S                             X                           A
DifL                        +                                          +           +  +
DifR          +                    +                   ++               +                   +
Ch L --001R00R000000RRG0000000QBGR000000000000000000000R000000000R000000RG00000000000RG0000QAAAAAB0000--
Ch R --001R000000000RRG00000R0QBGRG000000000000000000000000000000R000000RG000000000R0R000001AAAAABR000--
1
M
E
R
jpg image jpg image
jpg image Z-Score 35.0  RMSD 0.4A  (CBCA)
Ligand DMQ(DMP450)  Ki=25-fold against the wild-type
Muta   V                                 S                                              V
DifL         +              +                                                      +
DifR                        +                         +
Ch L --001R003000000RRG0000030QBGR000000000000000000000R000000000R00000RRG00000000030R00000QAAAAABR000--
Ch R --001R00R000000RRG0000000QBGR00000000000000000000OB000000000R00000RRG000000000R0R00000QAAAAABR000--
1
Q
B
S
jpg image jpg image
jpg image Z-Score 34.0  RMSD 0.5A  (CACB)
Ligand DMP(DMP323)  Ki=0.33nM
Muta   V                                 S                             X                           A
DifL         +              +                                          +
DifR                        +                         ++               +
Ch L --001R000000000RRG0000030QBGR000000000000000000000R000000000R00000ORG000000000R0R00000QAAAAABR000--
Ch R --001R00R000000RRG0000000QBGR000000000000000000000R000000000R00000ORG000000000R0R00000QAAAAABR000--
1
M
E
S
jpg image jpg image
jpg image Z-Score 34.7  RMSD 0.5A  (CBCA)
Ligand DMP(DMP323)  Ki=25-fold against the wild-type
Muta   V                                 S                                              V
DifL                        +                          +                                    +
DifR                                                  +
Ch L --001R00R000000RRG0000000QBGR000000000000000000000B000000000R00000RRG000000000R0R00000QBAAAABR000--
Ch R --001R00R000000RRG00000R0QBGR000000000000000000002B000000000R00000RRG000000000R0R00000QAAAAABR000--
1
M
E
T
jpg image jpg image
jpg image Z-Score 34.7  RMSD 0.5A  (CBCA)
Ligand DMP(DMP323)  Ki=0.5-fold against the wild-type
Muta   V                                 S                                            F
DifL         +              +                                          +
DifR       + +              +                         ++                           +
Ch L --001R000000000RRG0000000QBGR000000000000000000000R000000000R00000ORG000000000R0R00000QAAAAABR000--
Ch R --001RG00000000RRG0000000QBGR0000000000000000000030000000000R00000RRG00000000000R00000QAAAAABR000--
1
M
E
U
jpg image jpg image
jpg image Z-Score 34.8  RMSD 0.5A  (CBCA)
Ligand Ki=1000-fold against the wild-type
Muta   V                                 S                                            F
DifL                                                                               +
DifR     +                  +                         ++                +
Ch L --001R00R000000RRG00000R0QBGR000000000000000000000R000000000R00000RRG00000000000R00000QAAAAABR000--
Ch R --00RR00R000000RRG0000000QBGR00000000000000000000R0000000000R00000R0G000000000R0R00000QAAAAABR000--
1
P
R
O
jpg image jpg image
jpg image Z-Score 35.3  RMSD 0.4A  (CBCA)
Ligand A88(A-98881)  Ki=5pM
Muta  
DifL                              +
DifR  
Ch L --001R00R000000RRG00000R0QBGRG00000000000000000000R000000000R00000RRG000000000R0R00000QAAAAABR000--
Ch R --001R00R000000RRG00000R0QBGR00000000000000000000QB000000000R00000RRG000000000R0R00000QAAAAABR000--



[The D2 codes]

[The DSSP code]