Structure of PDB 8pnd Chain B Binding Site BS01

Receptor Information
>8pnd Chain B (length=326) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVIRVGTRKSQLARIQTDSVVATLKASYPGLQFEIIAMSTEKSLFTKEL
EHALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVG
KTLETLPEKSVVGTSSLRRAAQLQRKFPHLEFRSIQGNLNTRLRKLDEQQ
EFSAIILATAGLQRMGWHNRVGQILHPEECMYAVGQGALGVEVRAKDQDI
LDLVGVLHDPETLLRCIAERAFLRHLEGGCSVPVAVHTAMKDGQLYLTGG
VWSLDGSDSIQETMQATIHVPAQHEDGPEDDPQLVGITARNIPRGPQLAA
QNLGISLANLLLSKGAKNILDVARQL
Ligand information
Ligand IDZWW
InChIInChI=1S/C50H57N5O20/c1-22-28(12-46(66)67)24(3-8-42(58)59)34(52-22)18-38-31(15-49(72)73)26(5-10-44(62)63)36(54-38)20-40-32(16-50(74)75)27(6-11-45(64)65)37(55-40)19-39-30(14-48(70)71)25(4-9-43(60)61)35(53-39)17-33-29(13-47(68)69)23(21-51-33)2-7-41(56)57/h21,51-55H,2-20H2,1H3,(H,56,57)(H,58,59)(H,60,61)(H,62,63)(H,64,65)(H,66,67)(H,68,69)(H,70,71)(H,72,73)(H,74,75)
InChIKeyHFYKODBGFFMGCY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1c(c(c([nH]1)Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)Cc4c(c(c([nH]4)Cc5c(c(c[nH]5)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
CACTVS 3.385Cc1[nH]c(Cc2[nH]c(Cc3[nH]c(Cc4[nH]c(Cc5[nH]cc(CCC(O)=O)c5CC(O)=O)c(CCC(O)=O)c4CC(O)=O)c(CCC(O)=O)c3CC(O)=O)c(CCC(O)=O)c2CC(O)=O)c(CCC(O)=O)c1CC(O)=O
FormulaC50 H57 N5 O20
Name3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid
ChEMBL
DrugBank
ZINC
PDB chain8pnd Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8pnd One ring closer to a closure: the crystal structure of the ES 3 hydroxymethylbilane synthase intermediate.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		E73 K74 F77 S96 K98 D99 P101 T102 S146 S147 R149 R150 R173 L188 A189 V215 Q217 L254 G260 C261 S262
Binding residue
(residue number reindexed from 1)		E42 K43 F46 S65 K67 D68 P70 T71 S115 S116 R118 R119 R142 L157 A158 V184 Q186 L223 G229 C230 S231
Annotation score3
Enzymatic activity
Enzyme Commision number 2.5.1.61: hydroxymethylbilane synthase.
Gene Ontology
Molecular Function
GO:0004418 hydroxymethylbilane synthase activity
GO:0005515 protein binding
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:0006784 heme A biosynthetic process
GO:0006785 heme B biosynthetic process
GO:0018160 peptidyl-pyrromethane cofactor linkage
GO:0033014 tetrapyrrole biosynthetic process
GO:0048034 heme O biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8pnd, PDBe:8pnd, PDBj:8pnd
PDBsum8pnd
PubMed37863644
UniProtP08397|HEM3_HUMAN Porphobilinogen deaminase (Gene Name=HMBS)

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