Structure of PDB 6xpt Chain C Binding Site BS01

Receptor Information
>6xpt Chain C (length=154) 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
YEKA
Ligand information
Ligand IDUDP
InChIInChI=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
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=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 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[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 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain6xpt Chain C Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6xpt Nucleoside selectivity of Aspergillus fumigatus nucleoside-diphosphate kinase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		K11 F59 L63 R87 T93 V111 N114
Binding residue
(residue number reindexed from 1)		K12 F60 L64 R88 T94 V112 N115
Annotation score2
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:6xpt, PDBe:6xpt, PDBj:6xpt
PDBsum6xpt
PubMed33089641
UniProtQ7Z8P9|NDK_ASPFU Nucleoside diphosphate kinase (Gene Name=ndk1)

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