Structure of PDB 3iqe Chain D Binding Site BS01

Receptor Information
>3iqe Chain D (length=282) Species: 2320 (Methanopyrus kandleri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TVAKAIFIKCGNLGTSMMMDMLLDERADREDVEFRVVGTSVKMDPECVEA
AVEMALDIAEDFEPDFIVYGGPNPAAPGPSKAREMLADSEYPAVIIGDAP
GLKVKDEMEEQGLGYILVKPDAMLGARREFLDPVEMAIYNADLMKVLAAT
GVFRVVQEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFENPYAMV
KAMAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEMMRKAAELADEA
RELEKSNDAVLRTPHAPDGKVLSKRKFMEDPE
Ligand information
Ligand IDH4M
InChIInChI=1S/C31H45N6O16P/c1-13-22-14(2)36(12-37(22)23-27(33-13)34-31(32)35-28(23)45)16-5-3-15(4-6-16)9-17(38)24(42)18(39)10-50-30-26(44)25(43)20(52-30)11-51-54(48,49)53-19(29(46)47)7-8-21(40)41/h3-6,13-14,17-20,22,24-26,30,38-39,42-44H,7-12H2,1-2H3,(H,40,41)(H,46,47)(H,48,49)(H4,32,33,34,35,45)/t13-,14+,17-,18+,19?,20+,22+,24-,25+,26+,30-/m0/s1
InChIKeyGBMIGEWJAPFSQI-UQXKJNEMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@@H]1NC2=C(N3CN([C@H](C)[C@@H]13)c4ccc(C[C@H](O)[C@H](O)[C@H](O)CO[C@H]5O[C@H](CO[P](O)(=O)OC(CCC(O)=O)C(O)=O)[C@@H](O)[C@H]5O)cc4)C(=O)NC(=N2)N
ACDLabs 12.01N1=C(N)NC(C2=C1NC(C3N2CN(C3C)c4ccc(cc4)CC(C(O)C(O)COC5OC(COP(=O)(O)OC(CCC(=O)O)C(=O)O)C(O)C5O)O)C)=O
CACTVS 3.385C[CH]1NC2=C(N3CN([CH](C)[CH]13)c4ccc(C[CH](O)[CH](O)[CH](O)CO[CH]5O[CH](CO[P](O)(=O)OC(CCC(O)=O)C(O)=O)[CH](O)[CH]5O)cc4)C(=O)NC(=N2)N
OpenEye OEToolkits 1.7.6CC1C2C(N(CN2C3=C(N1)N=C(NC3=O)N)c4ccc(cc4)CC(C(C(COC5C(C(C(O5)COP(=O)(O)OC(CCC(=O)O)C(=O)O)O)O)O)O)O)C
OpenEye OEToolkits 1.7.6C[C@H]1[C@@H]2[C@H](N(CN2C3=C(N1)N=C(NC3=O)N)c4ccc(cc4)C[C@@H]([C@@H](C(CO[C@@H]5[C@@H]([C@@H]([C@H](O5)COP(=O)(O)OC(CCC(=O)O)C(=O)O)O)O)O)O)O)C
FormulaC31 H45 N6 O16 P
Name5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN
ChEMBL
DrugBank
ZINC
PDB chain3iqe Chain A Residue 284 [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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PDB3iqe Structural basis of the hydride transfer mechanism in F(420)-dependent methylenetetrahydromethanopterin dehydrogenase
Resolution1.8 Å
Binding residue
(original residue number in PDB)		E26 R27 A28
Binding residue
(residue number reindexed from 1)		E25 R26 A27
Annotation score4
Enzymatic activity
Enzyme Commision number 1.5.98.1: methylenetetrahydromethanopterin dehydrogenase.
Gene Ontology
Molecular Function
GO:0008901 ferredoxin hydrogenase activity
GO:0016491 oxidoreductase activity
GO:0030268 methylenetetrahydromethanopterin dehydrogenase activity
Biological Process
GO:0006730 one-carbon metabolic process
GO:0015948 methanogenesis
GO:0019386 methanogenesis, from carbon dioxide

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3iqe, PDBe:3iqe, PDBj:3iqe
PDBsum3iqe
PubMed19761261
UniProtP94951|MTD_METKA F420-dependent methylenetetrahydromethanopterin dehydrogenase (Gene Name=mtd)

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