Structure of PDB 8qw2 Chain B Binding Site BS01

Receptor Information

>8qw2 Chain B (length=152) Species: 9606 (Homo sapiens)

TGAHERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQASEELLRE
HYAELRERPFYGRLVKYMASGPVVAMVWQGLDVVRTSRALIGATNPADAP
PGTIRGDFCIEVGKNLIHGSDSVESARREIALWFRADELLCWEDSAGHWL
YE

Ligand information

• Ligand ID: UDP
• InChI: InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: XCCTYIAWTASOJW-XVFCMESISA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.370: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  CACTVS 3.370: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.7.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
• Formula: C9 H14 N2 O12 P2
• Name: URIDINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL130266
• DrugBank: DB03435
• ZINC: ZINC000004490939
• PDB chain: 8qw2 Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8qw2 Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes
• Resolution: 1.87 Å
• Binding residue (original residue number in PDB): K29 L72 F77 R105 T111 V129 N132
• Binding residue (residue number reindexed from 1): K12 L55 F60 R88 T94 V112 N115
• Annotation score: 2

External links

• PDB: RCSB:8qw2, PDBe:8qw2, PDBj:8qw2
• PDBsum: 8qw2
• UniProt: Q13232|NDK3_HUMAN Nucleoside diphosphate kinase 3 (Gene Name=NME3)