Structure of PDB 8dq9 Chain B Binding Site BS02

Receptor Information
>8dq9 Chain B (length=364) Species: 571 (Klebsiella oxytoca) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QDEMYMARALKLAARGRFTTHPNPNVGCVIVKDGEIVGEGFHYRAGEPHA
EVHALRMAGDKAKGATAYVTLEPCSHHTPPCCDALIAAGVARVVAAMQDP
NPQVAGRGLYRLQQAGIDVSHGLMMNEAEALNKGFLKRMRTGFPWIQLKM
GASLDGRTAMASGESQWITSPQARRDVQRLRAQSHAILTSSATVLADDPA
LTVRWQELSADTQALYPQENLRQPLRIVIDSQNRVTPEHRIIQQQGETLF
ARTHADERAWPDNVRTLLVPEHNGHLDLVLLMMQLGKQQVNSIWVEAGPT
LAGALLQAGLVDELIVYIAPKLLGSDARGLCALPGLEKLSQAPHFKFNEI
RQVGPDVCLHLTTA
Ligand information
Ligand IDGDP
InChIInChI=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
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=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 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(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
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain8dq9 Chain B Residue 403 [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]
PDB8dq9 Crystal structure of GDP bound 3-dehydroquinate dehydratase I from Klebsiella oxytoca
Resolution2.8 Å
Binding residue
(original residue number in PDB)		S201 S202 A203 S242 R245 H286 L289 T311 A315
Binding residue
(residue number reindexed from 1)		S190 S191 A192 S231 R234 H275 L278 T300 A304
Annotation score2
Enzymatic activity
Enzyme Commision number 1.1.1.193: 5-amino-6-(5-phosphoribosylamino)uracil reductase.
3.5.4.26: diaminohydroxyphosphoribosylaminopyrimidine deaminase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008270 zinc ion binding
GO:0008703 5-amino-6-(5-phosphoribosylamino)uracil reductase activity
GO:0008835 diaminohydroxyphosphoribosylaminopyrimidine deaminase activity
GO:0016491 oxidoreductase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0050661 NADP binding
Biological Process
GO:0009231 riboflavin biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8dq9, PDBe:8dq9, PDBj:8dq9
PDBsum8dq9
PubMed
UniProtA0A0H3FX83

[Back to BioLiP]