Structure of PDB 2ypn Chain A Binding Site BS01

Receptor Information
>2ypn 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]
DNVLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMVGLFVKELEVA
LLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDAL
PAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIIL
AVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAAL
NHHETALRVTAERAMNTRLEGGCQVPIGSYAELIDGEIWLRALVGAPDGS
QIIRGERRGAPQDAEQMGISLAEELLNNGAREILAEVYNGDAPA
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 chain2ypn 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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PDB2ypn Accurate and highly complete synchrotron protein crystal Laue diffraction data using the ESRF CCD and the Daresbury Laue software
Resolution2.3 Å
Binding residue
(original residue number in PDB)		S81 K83 D84 S128 S129 R131 R132 R155 L169 A170 C242
Binding residue
(residue number reindexed from 1)		S62 K64 D65 S109 S110 R112 R113 R136 L150 A151 C223
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) K64 D65 R112 R113 R130 R136 C223
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:2ypn, PDBe:2ypn, PDBj:2ypn
PDBsum2ypn
PubMed
UniProtP06983|HEM3_ECOLI Porphobilinogen deaminase (Gene Name=hemC)

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