Structure of PDB 4p8e Chain B Binding Site BS01

Receptor Information
>4p8e Chain B (length=217) Species: 243277 (Vibrio cholerae O1 biovar El Tor str. N16961) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMNQSSLLAEFGDPITRVENALQALREGRGVLLLDDEDRENEGDIIYAV
ESLTTAQMALMIRECSGIVCLCLTEAQADRLALPPMVVNNNSANQTAFTV
SIEAKHGVTTGVSAQDRVTTIKTAANPQAKPEDLARPGHVFPLRARAGGV
LARRGHTEGTVDLMQMAGLQPAGVLCELTNPDGSMAKTPEIIEFGKLHNM
PVLTIEDMVQYRIQFDL
Ligand information
Ligand ID5RP
InChIInChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5+/m1/s1
InChIKeyFNZLKVNUWIIPSJ-UHNVWZDZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OCC(=O)[C@H](O)[C@H](O)CO[P](O)(O)=O
OpenEye OEToolkits 1.5.0C(C(C(C(=O)CO)O)O)OP(=O)(O)O
CACTVS 3.341OCC(=O)[CH](O)[CH](O)CO[P](O)(O)=O
ACDLabs 10.04O=P(O)(O)OCC(O)C(O)C(=O)CO
OpenEye OEToolkits 1.5.0C([C@H]([C@H](C(=O)CO)O)O)OP(=O)(O)O
FormulaC5 H11 O8 P
NameRIBULOSE-5-PHOSPHATE
ChEMBL
DrugBank
ZINCZINC000001532567
PDB chain4p8e Chain B Residue 301 [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]
PDB4p8e Structural Basis for Competitive Inhibition of 3,4-Dihydroxy-2-butanone-4-phosphate Synthase from Vibrio cholerae.
Resolution2.04 Å
Binding residue
(original residue number in PDB)		R38 E39 D43 C68 T94 F96 R151 G153 H154 T155 L173 E175
Binding residue
(residue number reindexed from 1)		R40 E41 D45 C70 T96 F98 R153 G155 H156 T157 L175 E177
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E39 D43 C68 N92 F96 E101 H137 H154 E175
Catalytic site (residue number reindexed from 1) E41 D45 C70 N94 F98 E103 H139 H156 E177
Enzyme Commision number 4.1.99.12: 3,4-dihydroxy-2-butanone-4-phosphate synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0008686 3,4-dihydroxy-2-butanone-4-phosphate synthase activity
GO:0016829 lyase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
Biological Process
GO:0009231 riboflavin biosynthetic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4p8e, PDBe:4p8e, PDBj:4p8e
PDBsum4p8e
PubMed25792735
UniProtQ9KKP2|RIBB_VIBCH 3,4-dihydroxy-2-butanone 4-phosphate synthase (Gene Name=ribB)

[Back to BioLiP]