Structure of PDB 4u2k Chain D Binding Site BS01

Receptor Information
>4u2k Chain D (length=242) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVY
RAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVN
VGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHM
GVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLL
TMCASSGLKAGCVAGVIINRTQKETEARSIKVVVEAARKMLK
Ligand information
Ligand IDM5F
InChIInChI=1S/C7H11FN4O2/c8-5-3-12(2-4(10)1-9)7(14)11-6(5)13/h3-4H,1-2,9-10H2,(H,11,13,14)/t4-/m0/s1
InChIKeyZBKWVMMCABYTAU-BYPYZUCNSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FC1=CN(C(=O)NC1=O)CC(N)CN
CACTVS 3.385NC[CH](N)CN1C=C(F)C(=O)NC1=O
CACTVS 3.385NC[C@H](N)CN1C=C(F)C(=O)NC1=O
OpenEye OEToolkits 1.9.2C1=C(C(=O)NC(=O)N1CC(CN)N)F
OpenEye OEToolkits 1.9.2C1=C(C(=O)NC(=O)N1C[C@H](CN)N)F
FormulaC7 H11 F N4 O2
Name1-[(2S)-2,3-diaminopropyl]-5-fluoropyrimidine-2,4(1H,3H)-dione
ChEMBL
DrugBank
ZINCZINC000263621327
PDB chain4u2k Chain D Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4u2k X-ray structure uridine phosphorylase from Vibrio cholerae in complex with new anticancer compound at 1.17 A resolution
Resolution2.13 Å
Binding residue
(original residue number in PDB)		T94 G95 F161 Q165 F194 M196 I219
Binding residue
(residue number reindexed from 1)		T92 G93 F159 Q163 F192 M194 I217
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H7 G25 R29 R47 E79 R90 T93 R167 I219 I220 R222
Catalytic site (residue number reindexed from 1) H5 G23 R27 R45 E77 R88 T91 R165 I217 I218 R220
Enzyme Commision number 2.4.2.3: uridine phosphorylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004850 uridine phosphorylase activity
GO:0016757 glycosyltransferase activity
GO:0016763 pentosyltransferase activity
GO:0046872 metal ion binding
GO:0047847 deoxyuridine phosphorylase activity
Biological Process
GO:0009116 nucleoside metabolic process
GO:0009164 nucleoside catabolic process
GO:0009166 nucleotide catabolic process
GO:0044206 UMP salvage
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4u2k, PDBe:4u2k, PDBj:4u2k
PDBsum4u2k
PubMed
UniProtQ9K4U1

[Back to BioLiP]