Structure of PDB 2gyi Chain B Binding Site BS03

Receptor Information
>2gyi Chain B (length=385) Species: 1963 (Streptomyces olivochromogenes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YQPTPEDRFTFGLWTVGWQGRDPFGDATRPALDPVETVQRLAELGAHGVT
FHDDDLIPFGSSDTERESHIKRFRQALDATGMTVPMATTNLFTHPVFKDG
GFTANDRDVRRYALRKTIRNIDLAVELGAKTYVAWGGREGAESGAAKDVR
VALDRMKEAFDLLGEYVTSQGYDTRFAIEPKPNEPRGDILLPTVGHALAF
IERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQSGI
KYDQDLRFGAGDLRAAFWLVDLLESAGYEGPRHFDFKPPRTEDIDGVWAS
AAGCMRNYLILKERAAAFRADPEVQEALRASRLDELAQPTAADGVQELLA
DRTAFEDFDVDAAAARGMAFERLDQLAMDHLLGAR
Ligand information
Ligand IDHYA
InChIInChI=1S/C4H9NO5/c6-1-2(7)3(8)4(9)5-10/h2-3,6-8,10H,1H2,(H,5,9)/t2-,3+/m1/s1
InChIKeySJYJPXDRLWCEKB-GBXIJSLDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[CH](O)[CH](O)C(O)=NO
CACTVS 3.341OC[C@@H](O)[C@H](O)\C(O)=N\O
OpenEye OEToolkits 1.5.0C(C(C(C(=NO)O)O)O)O
ACDLabs 10.04N(/O)=C(/O)C(O)C(O)CO
OpenEye OEToolkits 1.5.0C([C@H]([C@@H](/C(=N/O)/O)O)O)O
FormulaC4 H9 N O5
Name2,3,4,N-TETRAHYDROXY-BUTYRIMIDIC ACID
ChEMBL
DrugBank
ZINC
PDB chain2gyi Chain B Residue 970 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2gyi Design, Synthesis, and Characterization of a Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, and High-Resolution X-Ray Crystallographic Structure of the Enzyme-Inhibitor Complex
Resolution1.6 Å
Binding residue
(original residue number in PDB)		H53 F93 W136 E180 D286
Binding residue
(residue number reindexed from 1)		H52 F92 W135 E179 D285
Annotation score1
Binding affinityMOAD: Ki<100nM
PDBbind-CN: -logKd/Ki=7.00,Ki<=100nM
Enzymatic activity
Catalytic site (original residue number in PDB) H53 D56 M87 E180 K182 E216 H219 D244 D254 D256 D286
Catalytic site (residue number reindexed from 1) H52 D55 M86 E179 K181 E215 H218 D243 D253 D255 D285
Enzyme Commision number 5.3.1.5: xylose isomerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0009045 xylose isomerase activity
GO:0016853 isomerase activity
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0042732 D-xylose metabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2gyi, PDBe:2gyi, PDBj:2gyi
PDBsum2gyi
PubMed7893671
UniProtP15587|XYLA_STROL Xylose isomerase (Gene Name=xylA)

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