Structure of PDB 4g0r Chain A Binding Site BS02

Receptor Information

>4g0r Chain A (length=554) Species: 10799 (H-1 parvovirus)

GIGVSTGTYDNQTTYKFLGDGWVEITAHASRLLHLGMPPSENYCRVTVHN
NQTTGHGTKVKGNMAYDDTHQQIWTPWSLVDANAWGVWFQPSDWQFIQNS
MESLNLDSLSQELFNVVVKTVTEQQGAGAIKVYNNDLTACMMVALDSNNI
LPYTPAAQTSETLGFYPWKPTAPAPYRYYFFMPRQLSVTSSNSAEGTQIT
DTIGEPQALNSQFFTIENTLPITLLRTGDEFTTGTYIFNTDPLKLTHTWQ
TNRHLGMPPRITDLPTSDTATASLTANGDRFGSTQTQNVNYVTEALRTRP
AQIGFMQPHDNFEANRGGPFKVPVVPLDITAGEDHDANGAIRFNYGKQHG
EDWAKQGAAPERYTWDAIDSAAGRDTARCFVQSAPISIPPNQNQILQRED
AIAGRTNMHYTNVFNSYGPLSAFPHPDPIYPNGQIWDKELDLEHKPRLHV
TAPFVCKNNPPGQLFVRLGPNLTDQFDPNSTTVSRIVTYSTFYWKGILKF
KAKLRPNLTWNPVYQATTDSVANSYMNVKKWLPSATGNMHSDPLICRPVP
HMTY

Ligand information

• Ligand ID: DC
• InChI: InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
• InChIKey: NCMVOABPESMRCP-SHYZEUOFSA-N
• SMILES:
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2
  OpenEye OEToolkits 1.5.0: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
  ACDLabs 10.04: O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
• Formula: C9 H14 N3 O7 P
• Name: 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL374699
• DrugBank: DB03798
• ZINC: ZINC000003861759
• PDB chain: 4g0r Chain A Residue 604

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4g0r Structural characterization of h-1 parvovirus: comparison of infectious virions to empty capsids.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): W59 K540
• Binding residue (residue number reindexed from 1): W22 K501
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005198 structural molecule activity

Cellular Component

• GO:0019028 viral capsid

External links

• PDB: RCSB:4g0r, PDBe:4g0r, PDBj:4g0r
• PDBsum: 4g0r
• PubMed: 23449783
• UniProt: P03136|CAPSD_PAVHH Capsid protein VP1