Structure of PDB 8qw2 Chain D Binding Site BS01

Receptor Information

>8qw2 Chain D (length=152) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

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

Software	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

PDB chain

8qw2 Chain D Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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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
PubMed
UniProt	Q13232\|NDK3_HUMAN Nucleoside diphosphate kinase 3 (Gene Name=NME3)

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