Structure of PDB 6xpu Chain A Binding Site BS01

Receptor Information
>6xpu Chain A (length=153) Species: 330879 (Aspergillus fumigatus Af293) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMSNEQTFIAIKPDGVQRGLIGPIISRFENRGFKLVAMKLVSPPQSQLEQ
HYADLSDKPFFKGLVSYMLSGPICAMVWEGRDVVKTGRTILGATNPLASA
PGTIRGDFAIDVGRNVCHGSDSVENAKKEIALWFKPEELISWKSATFDWV
YEK
Ligand information
Ligand IDIDP
InChIInChI=1S/C10H14N4O11P2/c15-6-4(1-23-27(21,22)25-26(18,19)20)24-10(7(6)16)14-3-13-5-8(14)11-2-12-9(5)17/h2-4,6-7,10,15-16H,1H2,(H,21,22)(H,11,12,17)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyJPXZQMKKFWMMGK-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O)O)O)N=CNC2=O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=CNC2=O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC=Nc23
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC=Nc23
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=CNC1=O)C(O)C3O
FormulaC10 H14 N4 O11 P2
NameINOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL1233551
DrugBank
ZINCZINC000004261903
PDB chain6xpu Chain A Residue 202 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6xpu Nucleoside selectivity of Aspergillus fumigatus nucleoside-diphosphate kinase.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		K11 L54 F59 R87 T93 V111 N114
Binding residue
(residue number reindexed from 1)		K12 L55 F60 R88 T94 V112 N115
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K11 Y51 N114 H117 E128
Catalytic site (residue number reindexed from 1) K12 Y52 N115 H118 E129
Enzyme Commision number 2.7.4.6: nucleoside-diphosphate kinase.
Gene Ontology
Molecular Function
GO:0004550 nucleoside diphosphate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0006183 GTP biosynthetic process
GO:0006228 UTP biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0009117 nucleotide metabolic process
GO:0009142 nucleoside triphosphate biosynthetic process
GO:0016310 phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6xpu, PDBe:6xpu, PDBj:6xpu
PDBsum6xpu
PubMed33089641
UniProtQ7Z8P9|NDK_ASPFU Nucleoside diphosphate kinase (Gene Name=ndk1)

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