Structure of PDB 1met Chain B Binding Site BS01

Receptor Information

>1met Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPFNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: DMP
• InChI: InChI=1S/C35H38N2O5/c38-23-29-15-11-27(12-16-29)21-36-31(19-25-7-3-1-4-8-25)33(40)34(41)32(20-26-9-5-2-6-10-26)37(35(36)42)22-28-13-17-30(24-39)18-14-28/h1-18,31-34,38-41H,19-24H2/t31-,32-,33+,34+/m1/s1
• InChIKey: XCVGQMUMMDXKCY-WZJLIZBTSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)CC2C(C(C(N(C(=O)N2Cc3ccc(cc3)CO)Cc4ccc(cc4)CO)Cc5ccccc5)O)O
  ACDLabs 10.04: O=C1N(C(C(O)C(O)C(N1Cc2ccc(cc2)CO)Cc3ccccc3)Cc4ccccc4)Cc5ccc(cc5)CO
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)C[C@@H]2[C@@H]([C@H]([C@H](N(C(=O)N2Cc3ccc(cc3)CO)Cc4ccc(cc4)CO)Cc5ccccc5)O)O
  CACTVS 3.341: OCc1ccc(CN2[C@H](Cc3ccccc3)[C@H](O)[C@@H](O)[C@@H](Cc4ccccc4)N(Cc5ccc(CO)cc5)C2=O)cc1
  CACTVS 3.341: OCc1ccc(CN2[CH](Cc3ccccc3)[CH](O)[CH](O)[CH](Cc4ccccc4)N(Cc5ccc(CO)cc5)C2=O)cc1
• Formula: C35 H38 N2 O5
• Name: [4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6-BIS(HYDROXY)-[1,3-BIS([4-HYDROXYMETHYL-PHENYL]METHYL)-4,7-BIS(PHEN YLMETHYL)]-2H-1,3-DIAZEPINONE;
  DMP323(INHIBITOR OF DUPONT MERCK)
• ChEMBL: CHEMBL21145
• ZINC: ZINC000003833858
• PDB chain: 1met Chain A Residue 323

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1met Molecular basis of HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with cyclic urea inhibitors.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D30 V32 G49 I50 P81 F82
• Binding residue (residue number reindexed from 1): D25 G27 A28 D30 V32 G49 I50 P81 F82
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=9.40,Ki=0.4nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D25 T26 G27
• 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

External links

• PDB: RCSB:1met, PDBe:1met, PDBj:1met
• PDBsum: 1met
• PubMed: 9048541
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)