Structure of PDB 1ypn Chain A Binding Site BS01

Receptor Information
>1ypn Chain A (length=294) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DNVLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMVTRGDVGQGLF
VKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNN
YDSLDALPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNG
EYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDDSRT
RELLAALNHHETALRVTAERAMNTRLEGGCQVPIGSYAELIDGEIWLRAL
VGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREILAEV
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 chain1ypn Chain A Residue 314 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ypn Time-Resolved Protein Crystal Diffraction: Determination by the Laue Method of the Behaviour of the Enzyme Hydroxymethylbilane Synthase (Lys59Gln Mutant) as It is Loaded with Substrate in the Crystal
Resolution2.3 Å
Binding residue
(original residue number in PDB)		S81 K83 D84 T127 S128 S129 R131 R132 R155 L169 A170 C242
Binding residue
(residue number reindexed from 1)		S69 K71 D72 T115 S116 S117 R119 R120 R143 L157 A158 C230
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) K71 D72 R119 R120 R137 R143 C230
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:1ypn, PDBe:1ypn, PDBj:1ypn
PDBsum1ypn
PubMed
UniProtP06983|HEM3_ECOLI Porphobilinogen deaminase (Gene Name=hemC)

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