Structure of PDB 3d8n Chain A Binding Site BS01

Receptor Information
>3d8n Chain A (length=250) Species: 262724 (Thermus thermophilus HB27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TMRIAYAGLRRKEEFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRELA
QGVDLFLATTGVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKE
AGLPPHAVGDGTSKSLLPLLPQGRGVAALQLYGKPLPLLENALAERGYRV
LPLMPYRHLPDPEGILRLEEAVLRGEVDALAFVAAIQVEFLFEGAKDPKA
LREALNTRVKALAVGRVTADALREWGVKPFYVDETERLGSLLQGFKRALQ
Ligand information
Ligand IDUP3
InChIInChI=1S/C40H38N4O16/c45-33(46)5-1-17-21(9-37(53)54)29-14-27-19(3-7-35(49)50)22(10-38(55)56)30(43-27)15-28-20(4-8-36(51)52)24(12-40(59)60)32(44-28)16-31-23(11-39(57)58)18(2-6-34(47)48)26(42-31)13-25(17)41-29/h13-16,41,44H,1-12H2,(H,45,46)(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)/b25-13?,26-13-,27-14-,28-15?,29-14-,30-15-,31-16-,32-16-
InChIKeyVZVFNUAIRVUCEW-XFMUOGEMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1c2c(c(c([nH]2)cc3nc(cc4c(c(c([nH]4)cc5nc1C(=C5CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)C(=C3CCC(=O)O)CC(=O)O)CC(=O)O)CCC(=O)O
ACDLabs 10.04O=C(O)CC1=C(c3nc1cc5nc(cc2nc(C(=C2CC(=O)O)CCC(=O)O)cc4c(c(c(c3)n4)CC(=O)O)CCC(=O)O)c(c5CCC(=O)O)CC(=O)O)CCC(=O)O
CACTVS 3.341OC(=O)CCc1c2[nH]c(cc3nc(cc4[nH]c(cc5nc(c2)c(CCC(O)=O)c5CC(O)=O)c(CC(O)=O)c4CCC(O)=O)c(CC(O)=O)c3CCC(O)=O)c1CC(O)=O
FormulaC40 H38 N4 O16
Name3,3',3'',3'''-[3,8,13,17-tetrakis(carboxymethyl)porphyrin-2,7,12,18-tetrayl]tetrapropanoic acid
ChEMBL
DrugBank
ZINC
PDB chain3d8n Chain A Residue 944 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3d8n Structure and mechanistic implications of a uroporphyrinogen III synthase-product complex.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		R9 Q31 T59 G60 V61 K92 Y131 G132 H157 V182 A183 A184 I185 Q186
Binding residue
(residue number reindexed from 1)		R10 Q32 T60 G61 V62 K93 Y132 G133 H158 V183 A184 A185 I186 Q187
Annotation score2
Enzymatic activity
Enzyme Commision number 4.2.1.75: uroporphyrinogen-III synthase.
Gene Ontology
Molecular Function
GO:0004852 uroporphyrinogen-III synthase activity
GO:0016829 lyase activity
Biological Process
GO:0006779 porphyrin-containing compound biosynthetic process
GO:0006780 uroporphyrinogen III biosynthetic process
GO:0033014 tetrapyrrole biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3d8n, PDBe:3d8n, PDBj:3d8n
PDBsum3d8n
PubMed18651750
UniProtQ72KM1

[Back to BioLiP]