Structure of PDB 4ivm Chain B Binding Site BS02

Receptor Information
>4ivm Chain B (length=464) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRTVVVLGGGISGLAASYHLSRAPCPPKVVLVESSERLGGWIRSVRGPNG
AIFELGPGGIRPAGALGARTLLLVSELGLDSEVLPVRGDHPAAQNRFLYV
GGALHALPTGLRPSPPFSKPLFWAGLRELTKPRGKEPDETVHSFAQRRLG
PEVASLAMDSLCRGVFAGNSRELSIRSCFPSLFQAEQTHRSILLGLLLGQ
PDSALIRQALAERWSQWSLRGGLEMLPQALETHLTSRGVSVLRGQPVCGL
SLQAEGRWKVSLRDSSLEADHVISAIPASVLSELLPAEAAPLARALSAIT
AVSVAVVNLQYQGAHLPVQGFGHLVPSSEDPGVLGIVYDSVAFPEQDGSP
PGLRVTVMLGGSWLQTLEASGCVLSQELFQQRAQEAAATQLGLKEMPSHC
LVHLHKNCIPQYTLGHWQKLESARQFLTAHRLPLTLAGASYEGVAVNDCI
ESGRQAAVSVLGTE
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain4ivm Chain B Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4ivm Quantitative structural insight into human variegate porphyria disease.
Resolution2.769 Å
Binding residue
(original residue number in PDB)		G9 G11 I12 S13 V33 E34 S35 G41 W42 G57 P58 P256 V257 I286 G448 A449 V454 A455 V456 C459
Binding residue
(residue number reindexed from 1)		G8 G10 I11 S12 V32 E33 S34 G40 W41 G56 P57 P246 V247 I276 G438 A439 V444 A445 V446 C449
Annotation score1
Enzymatic activity
Enzyme Commision number 1.3.3.4: protoporphyrinogen oxidase.
Gene Ontology
Molecular Function
GO:0004729 oxygen-dependent protoporphyrinogen oxidase activity
GO:0016491 oxidoreductase activity
GO:0050660 flavin adenine dinucleotide binding
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:0048034 heme O biosynthetic process
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005758 mitochondrial intermembrane space
GO:0031966 mitochondrial membrane

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ivm, PDBe:4ivm, PDBj:4ivm
PDBsum4ivm
PubMed23467411
UniProtP50336|PPOX_HUMAN Protoporphyrinogen oxidase (Gene Name=PPOX)

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