Structure of PDB 8qw0 Chain F Binding Site BS01

Receptor Information

>8qw0 Chain F (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 F 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 R122 V129 N132
Binding residue (residue number reindexed from 1)	K11 L54 F59 R87 T93 R104 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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