Structure of PDB 8cm5 Chain R Binding Site BS01

Receptor Information
>8cm5 Chain R (length=973) Species: 882 (Nitratidesulfovibrio vulgaris str. Hildenborough) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELQKLQWAKQTTSICCYCAVGCGLIVHTAKDGQGRAVNVEGDPDHPINEG
SLCPKGASIFQLGENDQRGTQPLYRAPFSDTWKPVTWDFALTEIAKRIKK
TRDASFTEKNAAGDLVNRTEAIASFGSAAMDNEECWAYGNILRSLGLVYI
EHQARICHSPTVPALAESFGRGAMTNHWNDLANSDCILIMGSNAAENHPI
AFKWVLRAKDKGATLIHVDPRFTRTSARCDVYAPIRSGADIPFLGGLIKY
ILDNKLYFTDYVREYTNASLIVGEKFSFKDGLFSGYDAANKKYDKSMWAF
ELDANGVPKRDPALKHPRCVINLLKKHYERYNLDKVAAITGTSKEQLQQV
YKAYAATGKPDKAGTIMYAMGWTQHSVGVQNIRAMAMIQLLLGNIGVAGG
GVNALRGESNVQGSTDQGLLAHIWPGYNPVPNSKAATLELYNAATPQSKD
PMSVNWWQNRPKYVASYLKALYPDEEPAAAYDYLPRIDAGRKLTDYFWLN
IFEKMDKGEFKGLFAWGMNPACGGANANKNRKAMGKLEWLVNVNLFENET
SSFWKGPGMNPAEIGTEVFFLPCCVSIEKEGSVANSGRWMQWRYRGPKPY
AETKPDGDIMLDMFKKVRELYAKEGGAYPAPIAKLNIADWEEHNEFSPTK
VAKLMNGYFLKDTEVGGKQFKKGQQVPSFAFLTADGSTCSGNWLHAGSFT
DAGNLMARRDKTQTPEQARIGLFPNWSFCWPVNRRILYNRASVDKTGKPW
NPAKAVIEWKDGKWVGDVVDGGGDPGTKHPFIMQTHGFGALYGPGREEGP
FPEHYEPLECPVSKNPFSKQLHNPVAFQIEGEKKAVADPRYPFIGTTYRV
TEHWQTGLMTRRCAWLVEAEPQIFCEISKELAKLRGIGNGDTVKVSSLRG
ALEAVAIVTERIRPFKIEGVDVHMVGLPWHYGWMVPKNGGDTANLLTPSA
GDPNTGIPETKAFMVDVRKVWSH
Ligand information
Ligand IDMGD
InChIInChI=1S/C20H26N10O13P2S2/c21-19-26-13-7(15(33)28-19)24-6-12(47)11(46)5(41-17(6)25-13)2-40-45(37,38)43-44(35,36)39-1-4-9(31)10(32)18(42-4)30-3-23-8-14(30)27-20(22)29-16(8)34/h3-6,9-10,17-18,24,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H4,21,25,26,28,33)/t4-,5-,6+,9-,10-,17-,18-/m1/s1
InChIKeyVQAGYJCYOLHZDH-ILXWUORBSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(=C(C5C(O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4C(=C([C@H]5[C@@H](O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
ACDLabs 10.04O=C1C=2NC3C(S)=C(S)C(OC3NC=2N=C(N)N1)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c5N=C(N)NC4=O)C(O)C6O
CACTVS 3.341NC1=NC2=C(N[C@@H]3[C@H](N2)O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
FormulaC20 H26 N10 O13 P2 S2
Name2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE;
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE
ChEMBL
DrugBank
ZINCZINC000195757106
PDB chain8cm5 Chain R Residue 1103 [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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PDB8cm5 W-formate dehydrogenase C872A from Desulfovibrio vulgaris - with Formamide
Resolution2.15 Å
Binding residue
(original residue number in PDB)
K90 G226 S227 N228 N232 D254 P255 R256 S272 D275 A404 M405 G406 H410 G442 E443 T881 Y883 R884 V885 T886 H888 W889 Q890 K996
Binding residue
(residue number reindexed from 1)
K55 G191 S192 N193 N197 D219 P220 R221 S237 D240 A369 M370 G371 H375 G407 E408 T846 Y848 R849 V850 T851 H853 W854 Q855 K961
Annotation score1
Enzymatic activity
Enzyme Commision number 1.2.1.2: Transferred entry: 1.17.1.9.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008863 formate dehydrogenase (NAD+) activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0030151 molybdenum ion binding
GO:0043546 molybdopterin cofactor binding
GO:0046872 metal ion binding
GO:0047111 formate dehydrogenase (cytochrome-c-553) activity
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0009061 anaerobic respiration
GO:0045333 cellular respiration
Cellular Component
GO:0042597 periplasmic space

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:8cm5, PDBe:8cm5, PDBj:8cm5
PDBsum8cm5
PubMed37985883
UniProtQ72EJ1

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