Structure of PDB 4mlv Chain A Binding Site BS02

Receptor Information
>4mlv Chain A (length=290) Species: 1404 (Priestia megaterium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMRKIIVGSRRSKLALTQTKWVIEQLKKQGLPFEFEIKEMVKEIEQAML
DKEIDMAVHSMKDMPAVLPEGLTIGCIPLREDHRDALISKNGERFEELPS
GAVIGTSSLRRGAQLLSMRSDIEIKWIRGNIDTRLEKLKNEDYDAIILAA
AGLSRMGWSKDTVTQYLEPEISVPAVGQGALAIECRENDHELLSLLQALN
HDETARAVRAERVFLKEMEGGCQVPIAGYGRILDGGNIELTSLVASPDGK
TIYKEHITGKDPIAIGSEAAERLTSQGAKLLIDRVKEELD
Ligand information
Ligand ID29P
InChIInChI=1S/C20H24N2O9/c1-9-12(6-18(27)28)10(2-4-16(23)24)14(21-9)8-15-13(7-19(29)30)11(20(31)22-15)3-5-17(25)26/h15,21H,2-8H2,1H3,(H,22,31)(H,23,24)(H,25,26)(H,27,28)(H,29,30)/t15-/m0/s1
InChIKeyDHEOBTWDCMSDOQ-HNNXBMFYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)CCc1c(nc(c1CC(=O)O)C)CC2C(=C(C(=O)N2)CCC(=O)O)CC(=O)O
OpenEye OEToolkits 1.7.6Cc1c(c(c([nH]1)CC2C(=C(C(=O)N2)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
OpenEye OEToolkits 1.7.6Cc1c(c(c([nH]1)C[C@H]2C(=C(C(=O)N2)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
CACTVS 3.385Cc1[nH]c(C[CH]2NC(=O)C(=C2CC(O)=O)CCC(O)=O)c(CCC(O)=O)c1CC(O)=O
CACTVS 3.385Cc1[nH]c(C[C@@H]2NC(=O)C(=C2CC(O)=O)CCC(O)=O)c(CCC(O)=O)c1CC(O)=O
FormulaC20 H24 N2 O9
Name3-[(5S)-5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]propanoic acid;
Dipyrromethanone
ChEMBL
DrugBank
ZINCZINC000098208116
PDB chain4mlv Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4mlv Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution.
Resolution1.455 Å
Binding residue
(original residue number in PDB)		R9 S11 L13 K81 D82 T125 S126 S127 R129 R130 R147 G148 N149 R153 C241
Binding residue
(residue number reindexed from 1)		R11 S13 L15 K62 D63 T106 S107 S108 R110 R111 R128 G129 N130 R134 C222
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K81 D82 R129 R130 R147 R153 C241
Catalytic site (residue number reindexed from 1) K62 D63 R110 R111 R128 R134 C222
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
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Cellular Component
External links
PDB RCSB:4mlv, PDBe:4mlv, PDBj:4mlv
PDBsum4mlv
PubMed24598743
UniProtQ8GCA8

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