Structure of PDB 5h6o Chain A Binding Site BS01

Receptor Information
>5h6o Chain A (length=281) Species: 666 (Vibrio cholerae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TPIRIATRQSPLALWQANYVKDALMAAHPGLQVELVTMVFVKELEIAMLE
GRADLAVHSMKDVPVDFPDGLGLVTICEREDPRDAFVSNTYAKIEDLPSG
AIVGTCSLRRQCQLKAARPDLVIKELRGNVGTRLSKLDAGEYDAIILAAA
GLKRLELESRIRSFIEPEQSLPAVGQGAVGIECRVNDQRVRALLAPLNHA
DTADRVRCERAMNLTLQGGCQVPIGSYALLEGDTIWLRALVGEPDGSQIV
RGEIRGPRTQAEQLGITLAEQLLSQGAKEIL
Ligand information
Ligand IDDPM
InChIInChI=1S/C20H24N2O8/c1-10-13(6-19(27)28)12(3-5-18(25)26)16(22-10)8-15-14(7-20(29)30)11(9-21-15)2-4-17(23)24/h9,21-22H,2-8H2,1H3,(H,23,24)(H,25,26)(H,27,28)(H,29,30)
InChIKeyLCAXMKQKEYTFDM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1[nH]c(Cc2[nH]cc(CCC(O)=O)c2CC(O)=O)c(CCC(O)=O)c1CC(O)=O
OpenEye OEToolkits 1.7.6Cc1c(c(c([nH]1)Cc2c(c(c[nH]2)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
ACDLabs 12.01O=C(O)Cc1c(ncc1CCC(=O)O)Cc2c(c(c(n2)C)CC(=O)O)CCC(=O)O
FormulaC20 H24 N2 O8
Name3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid;
DIPYRROMETHANE COFACTOR
ChEMBL
DrugBankDB04517
ZINCZINC000015277485
PDB chain5h6o Chain A 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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PDB5h6o Porphobilinogen deaminase from Vibrio Cholerae
Resolution2.702 Å
Binding residue
(original residue number in PDB)		S87 K89 D90 C134 S135 R137 R138 R161 A176 Q204 G205 C248
Binding residue
(residue number reindexed from 1)		S59 K61 D62 C106 S107 R109 R110 R133 A148 Q176 G177 C220
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K89 D90 R137 R138 R155 R161 C248
Catalytic site (residue number reindexed from 1) K61 D62 R109 R110 R127 R133 C220
Enzyme Commision number 2.5.1.61: hydroxymethylbilane synthase.
Gene Ontology
Molecular Function
GO:0004418 hydroxymethylbilane synthase activity
GO:0016740 transferase activity
Biological Process
GO:0006779 porphyrin-containing compound biosynthetic process
GO:0006782 protoporphyrinogen IX biosynthetic process
GO:0006783 heme biosynthetic process
GO:0018160 peptidyl-pyrromethane cofactor linkage
GO:0033014 tetrapyrrole biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5h6o, PDBe:5h6o, PDBj:5h6o
PDBsum5h6o
PubMed
UniProtQ9KVM1|HEM3_VIBCH Porphobilinogen deaminase (Gene Name=hemC)

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