Structure of PDB 2lyb Chain A Binding Site BS01

Receptor Information

>2lyb Chain A (length=131) Species: 11698 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE))

GARASVLSGGELDKWEKIRLRPGGKKQYKLKHIVWASRELERFAVNPGLL
ETSEGCRQILGQLQPSLQTGSEELRSLYNTIAVLYCVHQRIDVKDTKEAL
DKIEEEQNKSKKKAQQAAADTGNNSQVSQNY

Ligand information

• Ligand ID: 8SP
• InChI: InChI=1S/C22H42NO10P/c1-3-5-7-9-11-13-20(24)30-15-18(33-21(25)14-12-10-8-6-4-2)16-31-34(28,29)32-17-19(23)22(26)27/h18-19H,3-17,23H2,1-2H3,(H,26,27)(H,28,29)/t18-,19+/m1/s1
• InChIKey: TWOCGGYLNFTSJO-MOPGFXCFSA-N
• SMILES:
  CACTVS 3.370: CCCCCCCC(=O)OC[CH](CO[P](O)(=O)OC[CH](N)C(O)=O)OC(=O)CCCCCCC
  OpenEye OEToolkits 1.7.6: CCCCCCCC(=O)OCC(COP(=O)(O)OCC(C(=O)O)N)OC(=O)CCCCCCC
  OpenEye OEToolkits 1.7.6: CCCCCCCC(=O)OC[C@H](COP(=O)(O)OC[C@@H](C(=O)O)N)OC(=O)CCCCCCC
  CACTVS 3.370: CCCCCCCC(=O)OC[C@H](CO[P](O)(=O)OC[C@H](N)C(O)=O)OC(=O)CCCCCCC
  ACDLabs 12.01: O=C(OC(COP(=O)(OCC(C(=O)O)N)O)COC(=O)CCCCCCC)CCCCCCC
• Formula: C22 H42 N O10 P
• Name: O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
• PDB chain: 2lyb Chain A Residue 300

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2lyb Trio engagement via plasma membrane phospholipids and the myristoyl moiety governs HIV-1 matrix binding to bilayers.
• Resolution: N/A
• Binding residue (original residue number in PDB): F44 L64
• Binding residue (residue number reindexed from 1): F43 L63
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=4.46,Kd=35uM

Enzymatic activity

• 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:0005198 structural molecule activity

External links

• PDB: RCSB:2lyb, PDBe:2lyb, PDBj:2lyb
• PDBsum: 2lyb
• PubMed: 23401539
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)