Structure of PDB 8qw0 Chain D Binding Site BS01

Receptor Information

>8qw0 Chain D (length=151) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GAHERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQASEELLREH
YAELRERPFYGRLVKYMASGPVVAMVWQGLDVVRTSRALIGATNPADAPP
GTIRGDFCIEVGKNLIHGSDSVESARREIALWFRADELLCWEDSAGHWLY
E

Ligand information

Ligand ID

GDP

InChI

InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1

InChIKey

QGWNDRXFNXRZMB-UUOKFMHZSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385	NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385	NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6	c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N

Formula

C10 H15 N5 O11 P2

Name

GUANOSINE-5'-DIPHOSPHATE

PDB chain

8qw0 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	8qw0 Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes
Resolution	2.175 Å
Binding residue (original residue number in PDB)	K29 L72 F77 R105 T111 V129 N132
Binding residue (residue number reindexed from 1)	K11 L54 F59 R87 T93 V111 N114
Annotation score	3

External links

PDB	RCSB:8qw0, PDBe:8qw0, PDBj:8qw0
PDBsum	8qw0
PubMed
UniProt	Q13232\|NDK3_HUMAN Nucleoside diphosphate kinase 3 (Gene Name=NME3)

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