Structure of PDB 4jjf Chain B Binding Site BS01

Receptor Information
>4jjf Chain B (length=344) Species: 79929 (Methanothermobacter marburgensis str. Marburg) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLAILGAGCYRTHAASGITNFSRACEVAEMVGKPEIAMTHSTITMGAEL
KELAGVDEVVVADPVFDNQFTVIDDFAYEDVIEAHKEDPEKIMPQIREKV
NEVAKELPKPPEGAIHFTHPEDLGFEITTDDREAVADADFIMTWFPKGDM
QPDIINKFIDDIKPGAIVTHACTIPTTKFYKIFEQKHGDLVTKPETLNVT
SYHPGAVPEMKGQVYIAEGYASEDAIETLFELGQKARGNAYRLPAELLGP
VCDMCSALTAITYAGILSYRDSVTQVLGAPASFAQMMAKESLEQITALME
KVGIDKMEENLDPGALLGTADSMNFGASAEILPTVFEILEKRKK
Ligand information
Ligand IDFE9
InChIInChI=1S/C19H22N6O10P.2CO.Fe.H2O.H2S/c1-7-9(3-4-26)22-16(29)8(2)14(7)35-36(31,32)33-5-10-12(27)13(28)18(34-10)25-6-21-11-15(25)23-19(20)24-17(11)30;2*1-2;;;/h6,10,12-13,18,27-28H,3,5H2,1-2H3,(H5,20,22,23,24,29,30,31,32);;;;2*1H2/q;2*+1;+5;;/p-3/t10-,12-,13-,18-;;;;;/m1...../s1
InChIKeyAEHOAZNVUAGELD-VPXBKTNXSA-K
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1=C2CC(=O)[Fe+2](N2C(=O)C(=C1OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4N=C(NC5=O)N)O)O)C)(C#[O+])(C#[O+])(O)S
CACTVS 3.385CC1=C(O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N)C(=C5CC(=O)[Fe++](O)(S)(C#[O+])(C#[O+])N5C1=O)C
OpenEye OEToolkits 1.7.6CC1=C2CC(=O)[Fe+2](N2C(=O)C(=C1OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4N=C(NC5=O)N)O)O)C)(C#[O+])(C#[O+])(O)S
CACTVS 3.385CC1=C(O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N)C(=C5CC(=O)[Fe++](O)(S)(C#[O+])(C#[O+])N5C1=O)C
FormulaC21 H23 Fe N6 O13 P S
Nameiron-guanylyl pyridinol cofactor
ChEMBL
DrugBank
ZINC
PDB chain4jjf Chain B Residue 401 [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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PDB4jjf Crystal structures of [fe]-hydrogenase in complex with inhibitory isocyanides: implications for the h2 -activation site.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		L6 G7 G9 A62 D63 P64 P110 P111 D131 W144 F145 P146 I154 A171 C172 P204 A206
Binding residue
(residue number reindexed from 1)		L6 G7 G9 A62 D63 P64 P110 P111 D131 W144 F145 P146 I154 A171 C172 P204 A206
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.00,Ki=10nM
Enzymatic activity
Enzyme Commision number 1.12.98.2: 5,10-methenyltetrahydromethanopterin hydrogenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0047068 N5,N10-methenyltetrahydromethanopterin hydrogenase 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:4jjf, PDBe:4jjf, PDBj:4jjf
PDBsum4jjf
PubMed23873755
UniProtP32440|HMD_METTM 5,10-methenyltetrahydromethanopterin hydrogenase (Gene Name=hmd)

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