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Structure of PDB 4h4m Chain A Binding Site BS01

Receptor Information

>4h4m Chain A (length=548) Species: 11678 (Human immunodeficiency virus type 1 BH10)

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLP
QGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRET
KLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQ
YALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQV

Ligand information

• Ligand ID: 494
• InChI: InChI=1S/C21H15Cl2N3O4/c22-15-3-4-18(30-17-11-14(2-1-6-24)10-16(23)12-17)19(13-15)29-9-8-26-7-5-20(27)25-21(26)28/h1-5,7,10-13H,8-9H2,(H,25,27,28)/b2-1+
• InChIKey: LXPGWIGXHHBGJC-OWOJBTEDSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1cc(c(cc1Cl)OCCN2C=CC(=O)NC2=O)Oc3cc(cc(c3)Cl)/C=C/C#N
  OpenEye OEToolkits 1.7.6: c1cc(c(cc1Cl)OCCN2C=CC(=O)NC2=O)Oc3cc(cc(c3)Cl)C=CC#N
  CACTVS 3.370: Clc1ccc(Oc2cc(Cl)cc(\C=C\C#N)c2)c(OCCN3C=CC(=O)NC3=O)c1
  CACTVS 3.370: Clc1ccc(Oc2cc(Cl)cc(C=CC#N)c2)c(OCCN3C=CC(=O)NC3=O)c1
  ACDLabs 12.01: N#C\C=C\c3cc(Oc2ccc(Cl)cc2OCCN1C=CC(=O)NC1=O)cc(Cl)c3
• Formula: C21 H15 Cl2 N3 O4
• Name: (2E)-3-(3-chloro-5-{4-chloro-2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop-2-enenitrile
• ChEMBL: CHEMBL1923490
• ZINC: ZINC000073196585
• PDB chain: 4h4m Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4h4m Crystal Structures of HIV-1 Reverse Transcriptase with Picomolar Inhibitors Reveal Key Interactions for Drug Design.
• Resolution: 2.85 Å
• Binding residue (original residue number in PDB): P95 L100 K102 K103 V106 V108 Y181 Y188 W229 L234 P236 Y318
• Binding residue (residue number reindexed from 1): P95 L100 K102 K103 V106 V108 Y181 Y188 W229 L234 P236 Y318
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.52,IC50=3.0nM

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:0003676 nucleic acid binding
• GO:0003964 RNA-directed DNA polymerase activity
• GO:0004523 RNA-DNA hybrid ribonuclease activity

Biological Process

• GO:0006278 RNA-templated DNA biosynthetic process

External links

• PDB: RCSB:4h4m, PDBe:4h4m, PDBj:4h4m
• PDBsum: 4h4m
• PubMed: 23163887
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)

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