Structure of PDB 1m0b Chain B Binding Site BS01

Receptor Information

>1m0b Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: 0ZQ
• InChI: InChI=1S/C38H49N5O7/c1-38(2,3)50-37(49)41-29(23-26-13-7-4-8-14-26)21-22-40-32(25-28-17-11-6-12-18-28)36(48)42-30(19-20-33(44)45)35(47)43-31(34(39)46)24-27-15-9-5-10-16-27/h4-18,29-32,40H,19-25H2,1-3H3,(H2,39,46)(H,41,49)(H,42,48)(H,43,47)(H,44,45)/t29-,30+,31+,32+/m1/s1
• InChIKey: CBWQRQVEXJTNOT-ZLESDFJESA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CC(C)(C)OC(=O)NC(CCNC(Cc1ccccc1)C(=O)NC(CCC(=O)O)C(=O)NC(Cc2ccccc2)C(=O)N)Cc3ccccc3
  CACTVS 3.370: CC(C)(C)OC(=O)N[C@H](CCN[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](Cc2ccccc2)C(N)=O)Cc3ccccc3
  ACDLabs 12.01: O=C(N)C(NC(=O)C(NC(=O)C(NCCC(NC(=O)OC(C)(C)C)Cc1ccccc1)Cc2ccccc2)CCC(=O)O)Cc3ccccc3
  CACTVS 3.370: CC(C)(C)OC(=O)N[CH](CCN[CH](Cc1ccccc1)C(=O)N[CH](CCC(O)=O)C(=O)N[CH](Cc2ccccc2)C(N)=O)Cc3ccccc3
  OpenEye OEToolkits 1.7.0: CC(C)(C)OC(=O)N[C@H](CCN[C@@H](Cc1ccccc1)C(=O)N[C@@H](CCC(=O)O)C(=O)N[C@@H](Cc2ccccc2)C(=O)N)Cc3ccccc3
• Formula: C38 H49 N5 O7
• Name: N-{(3S)-3-[(tert-butoxycarbonyl)amino]-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide
• ChEMBL: CHEMBL215431
• ZINC: ZINC000049942301
• PDB chain: 1m0b Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1m0b Role of hydroxyl group and R/S configuration of isostere in binding properties of HIV-1 protease inhibitors
• Resolution: 2.45 Å
• Binding residue (original residue number in PDB): D125 G127 A128 D130 G148 G149 P181 V182 I184
• Binding residue (residue number reindexed from 1): D25 G27 A28 D30 G48 G49 P81 V82 I84
• Annotation score: 1
• Binding affinity: MOAD: Ki=1.53nM
  PDBbind-CN: -logKd/Ki=8.82,Ki=1.53nM

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

External links

• PDB: RCSB:1m0b, PDBe:1m0b, PDBj:1m0b
• PDBsum: 1m0b
• PubMed: 15560786
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)