Structure of PDB 1dmr Chain A Binding Site BS01

Receptor Information
>1dmr Chain A (length=779) Species: 1061 (Rhodobacter capsulatus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LANGTVMSGSHWGVFTATVENGRATAFTPWEKDPHPSPMLAGVLDSIYSP
TRIKYPMVRREFLEKGVNADRSTRGNGDFVRVSWDQALDLVAAEVKRVEE
TYGPEGVFGGSYGWKSPGRLHNCTTLLRRMLTLAGGYVNGAGDYSTGAAQ
VIMPHVVGTLEVYEQQTAWPVLAENTEVMVFWAADPIKTSQIGWVIPEHG
AYPGLEALKAKGTKVIVIDPVRTKTVEFFGAEHITPKPQTDVAIMLGMAH
TLVAEDLYDKDFIANYTSGFDKFLPYLDGETDSTPKTAEWAEGISGVPAE
TIKELARLFESKRTMLAAGWSMQRMHHGEQAHWMLVTLASMLGQIGLPGG
GFGLSYHYSGGGTPSTSGPALAGITDGGAATKGPEWLAASGASVIPVARV
VDMLENPGAEFDFNGTRSKFPDVKMAYWVGGNPFVHHQDRNRMVKAWEKL
ETFVVHDFQWTPTARHADIVLPATTSYERNDIETIGDYSNTGILAMKKIV
EPLYEARSDYDIFAAVAERLGKGAEFTEGKDEMGWIKSFYDDAAKQGKAA
GVQMPAFDAFWAEGIVEFPVTDGADFVRYASFREDPLLNPLGTPTGLIEI
YSKNIEKMGYDDCPAHPTWMEPLERLDGPGAKYPLHIAASHPFNRLHSQL
NGTVLREGYAVQGHEPCLMHPDDAAARGIADGDVVRVHNDRGQILTGVKV
TDAVMKGVIQIYEGGWYDPSDVTEPGTLDKYGDVNVLSADIGTSKLAQGN
CGQTVLAEVEKYTGPAVTLTGFVAPKAAE
Ligand information
Ligand IDPGD
InChIInChI=1S/C20H24N10O13P2S2/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/h3-6,9-10,17-18,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H3,21,25,26,28,33)/t4-,5-,6+,9-,10-,17-,18-/m1/s1
InChIKeySOFMTHSWCZNJTQ-ILXWUORBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(=C(C5C(O4)NC6=NC(=NC(=O)C6=N5)N)S)S)O)O)N=C(NC2=O)N
ACDLabs 10.04O=C6N=C(N=C1C6=NC2C(S)=C(S)C(OC2N1)COP(=O)(O)OP(=O)(O)OCC5OC(n4cnc3c4N=C(N)NC3=O)C(O)C5O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]5NC6=NC(=NC(=O)C6=N[C@H]5C(=C4S)S)N)[C@@H](O)[C@H]3O
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=NC(=NC(=O)C6=N5)N)S)S)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]5NC6=NC(=NC(=O)C6=N[CH]5C(=C4S)S)N)[CH](O)[CH]3O
FormulaC20 H24 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
ChEMBL
DrugBank
ZINCZINC000195756841
PDB chain1dmr Chain A Residue 782 [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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PDB1dmr Molybdenum Active Centre of Dmso Reductase from Rhodobacter Capsulatus: Crystal Structure of the Oxidised Enzyme at 1.82-A Resolution and the Dithionite-Reduced Enzyme at 2.8-A Resolution
Resolution1.82 Å
Binding residue
(original residue number in PDB)		Y114 G115 W116 K117 S118 C125 Y146 S147 R326 G432 G433 N434 H438 H458 D459 F460 D511 A641 H643 H649 S650 Q651 E715 N737 G754
Binding residue
(residue number reindexed from 1)		Y112 G113 W114 K115 S116 C123 Y144 S145 R324 G430 G431 N432 H436 H456 D457 F458 D509 A639 H641 H647 S648 Q649 E713 N735 G752
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) M41 Y114 W116 D145 S147 T148 V153 I154 W322 S357 Y358 H359 Y360
Catalytic site (residue number reindexed from 1) M39 Y112 W114 D143 S145 T146 V151 I152 W320 S355 Y356 H357 Y358
Enzyme Commision number 1.7.2.3: trimethylamine-N-oxide reductase.
1.8.5.3: respiratory dimethylsulfoxide reductase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0043546 molybdopterin cofactor binding

View graph for
Molecular Function
External links
PDB RCSB:1dmr, PDBe:1dmr, PDBj:1dmr
PDBsum1dmr
PubMed
UniProtQ52675|DSTOR_RHOCA Dimethyl sulfoxide/trimethylamine N-oxide reductase (Gene Name=dorA)

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