Structure of PDB 8rc9 Chain A Binding Site BS01

Receptor Information
>8rc9 Chain A (length=966) 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
FPEHYEPLECPVSKNPFSKQLHNPVAKAVCDPRYPFIGTTYRVTEHWQTG
LMTRRCAWLVEAEPQIFCEISKELAKLRGIGNGDTVKVSSLRGALEAVAI
VTERIRPFKIEGVDVHMVGLPWHYGWMVPKNGGDTANLLTPSADPNTGIP
ETKAFMVDVRKVWSHP
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 chain8rc9 Chain A Residue 1101 [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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PDB8rc9 Substrate-dependent oxidative inactivation of a W-dependent formate dehydrogenase involving selenocysteine displacement
Resolution2.06 Å
Binding residue
(original residue number in PDB)
K90 S227 N228 N232 D254 P255 R256 S272 D275 A404 M405 G406 W407 G442 Y883 R884 T886 H888 W889 Q890 K996
Binding residue
(residue number reindexed from 1)
K55 S192 N193 N197 D219 P220 R221 S237 D240 A369 M370 G371 W372 G407 Y841 R842 T844 H846 W847 Q848 K953
Annotation score4
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0030151 molybdenum ion binding
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0009061 anaerobic 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:8rc9, PDBe:8rc9, PDBj:8rc9
PDBsum8rc9
PubMed39148770
UniProtQ72EJ1

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