Structure of PDB 4d9m Chain B Binding Site BS01

Receptor Information
>4d9m Chain B (length=383) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVFSLKIDIADNKFFNGETSPLFSQSQAKLARQFHQKIAGYRPTPLCALD
DLANLFGVKKILVKDESKRFGLNAFKMLGGAYAIAQLLCEKYHLDIETLS
FEEKMTFATTTDGNHGRGVAWAAQQLGQNAVIYMPKGSAQERVDAILNLG
AECIVTDMNYDDTVRLTMQHAQQHGWEVVQDTAWEGYTKIPTWIMQGYAT
LADEAVEQMREMGVTPTHVLLQAGVGAMAGGVLGYLVDVYSPQNLHSIIV
EPDKADCIYRSGVKGDIVATIMAGLACGEPNPLGWEILRNCATQFISCQD
SVAALGMRVLGNPYGNDPRIISGESGAVGLGVLAAVHYHPQRQSLMEKLA
LNKDAVVLVISTEGDTDVKHYREVVWEGKHAVA
Ligand information
Ligand ID0JO
InChIInChI=1S/C11H13N2O7P/c1-6-10(14)9(4-13-7(2)11(15)16)8(3-12-6)5-20-21(17,18)19/h3-4,14H,2,5H2,1H3,(H,15,16)(H2,17,18,19)/b13-4+
InChIKeyBHIGINKEEFZJGX-YIXHJXPBSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OCc1cnc(c(O)c1/C=N/C(=C)C(=O)O)C
CACTVS 3.370Cc1ncc(CO[P](O)(O)=O)c(C=NC(=C)C(O)=O)c1O
OpenEye OEToolkits 1.7.6Cc1c(c(c(cn1)COP(=O)(O)O)C=NC(=C)C(=O)O)O
OpenEye OEToolkits 1.7.6Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/C(=C)C(=O)O)O
FormulaC11 H13 N2 O7 P
Name2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid
ChEMBL
DrugBank
ZINCZINC000098207815
PDB chain4d9m Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4d9m Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis
Resolution2.5 Å
Binding residue
(original residue number in PDB)		K77 T119 D120 N122 H123 G232 V233 G234 A235 M236 G288 L289 T376 E377
Binding residue
(residue number reindexed from 1)		K76 T111 D112 N114 H115 G224 V225 G226 A227 M228 G274 L275 T362 E363
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K77 T376
Catalytic site (residue number reindexed from 1) K76 T362
Enzyme Commision number 4.3.1.15: diaminopropionate ammonia-lyase.
Gene Ontology
Molecular Function
GO:0008838 diaminopropionate ammonia-lyase activity
GO:0016829 lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0042803 protein homodimerization activity

View graph for
Molecular Function
External links
PDB RCSB:4d9m, PDBe:4d9m, PDBj:4d9m
PDBsum4d9m
PubMed22505717
UniProtP66899|DPAL_ECOLI Diaminopropionate ammonia-lyase (Gene Name=ygeX)

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