Structure of PDB 1pda Chain A Binding Site BS01

Receptor Information
>1pda Chain A (length=296) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DNVLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMVTRGDVIGKGL
FVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSN
NYDSLDALPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDN
GEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDDSR
TRELLAALNHHETALRVTAERAMNTRLEGACQVPIGSYAELIDGEIWLRG
LVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREILAEVY
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 chain1pda Chain A Residue 314 [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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PDB1pda Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site.
Resolution1.76 Å
Binding residue
(original residue number in PDB)		R11 S13 F62 K83 D84 T127 S128 S129 R131 R132 R149 G150 N151 V152 R155 C242
Binding residue
(residue number reindexed from 1)		R9 S11 F51 K72 D73 T116 S117 S118 R120 R121 R138 G139 N140 V141 R144 C231
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K83 D84 R131 R132 R149 R155 C242
Catalytic site (residue number reindexed from 1) K72 D73 R120 R121 R138 R144 C231
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
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1pda, PDBe:1pda, PDBj:1pda
PDBsum1pda
PubMed1522882
UniProtP06983|HEM3_ECOLI Porphobilinogen deaminase (Gene Name=hemC)

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