Structure of PDB 4cpt Chain B Binding Site BS01

Receptor Information
>4cpt Chain B (length=99) Species: 12721 (Human immunodeficiency virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPTNVIGRNLLTQIGCTLNF
Ligand information
Ligand ID1T8
InChIInChI=1S/C41H54N6O6/c1-28(2)34-36(48)43-23-8-7-11-29-13-15-30(16-14-29)25-41(52,38(50)44-34)21-10-24-47(46-37(49)35(40(3,4)5)45-39(51)53-6)27-31-17-19-32(20-18-31)33-12-9-22-42-26-33/h7-9,12-20,22,26,28,34-35,52H,10-11,21,23-25,27H2,1-6H3,(H,43,48)(H,44,50)(H,45,51)(H,46,49)/b8-7-/t34-,35+,41+/m0/s1
InChIKeyNKAIBDUEJMTLGH-UGLCWRDGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COC(=O)N[CH](C(=O)NN(CCC[C]1(O)Cc2ccc(CC=CCNC(=O)[CH](NC1=O)C(C)C)cc2)Cc3ccc(cc3)c4cccnc4)C(C)(C)C
OpenEye OEToolkits 1.7.6CC(C)C1C(=O)NCC=CCc2ccc(cc2)CC(C(=O)N1)(CCCN(Cc3ccc(cc3)c4cccnc4)NC(=O)C(C(C)(C)C)NC(=O)OC)O
OpenEye OEToolkits 1.7.6CC(C)[C@H]1C(=O)NC/C=C\Cc2ccc(cc2)C[C@@](C(=O)N1)(CCCN(Cc3ccc(cc3)c4cccnc4)NC(=O)[C@H](C(C)(C)C)NC(=O)OC)O
ACDLabs 12.01O=C(OC)NC(C(=O)NN(Cc2ccc(c1cccnc1)cc2)CCCC4(O)C(=O)NC(C(=O)NCC=CCc3ccc(cc3)C4)C(C)C)C(C)(C)C
CACTVS 3.385COC(=O)N[C@H](C(=O)NN(CCC[C@@]1(O)Cc2ccc(C\C=C/CNC(=O)[C@@H](NC1=O)C(C)C)cc2)Cc3ccc(cc3)c4cccnc4)C(C)(C)C
FormulaC41 H54 N6 O6
Name
ChEMBL
DrugBank
ZINCZINC000263620796
PDB chain4cpt Chain B Residue 1202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4cpt Synthesis of P1'-Functionalized Macrocyclic Transition-State Mimicking HIV-1 Protease Inhibitors Encompassing a Tertiary Alcohol.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		L123 D125 G127 A128 D129 G148 G149 F153
Binding residue
(residue number reindexed from 1)		L23 D25 G27 A28 D29 G48 G49 F53
Annotation score1
Binding affinityMOAD: Ki=20nM
PDBbind-CN: -logKd/Ki=7.70,Ki=20nM
Enzymatic activity
Catalytic site (original residue number in PDB) D125 T126 G127
Catalytic site (residue number reindexed from 1) D25 T26 G27
Enzyme Commision number 2.7.7.-
2.7.7.49: RNA-directed DNA polymerase.
2.7.7.7: DNA-directed DNA polymerase.
3.1.-.-
3.1.13.2: exoribonuclease H.
3.1.26.13: retroviral ribonuclease H.
3.4.23.16: HIV-1 retropepsin.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:4cpt, PDBe:4cpt, PDBj:4cpt
PDBsum4cpt
PubMed25054811
UniProtP03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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