Structure of PDB 7rdf Chain A Binding Site BS01

Receptor Information
>7rdf Chain A (length=375) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIEADYLVIGAGIAGASTGYWLSAHGRVVVLEREAQPGYHSTGRSAAHYT
VAYGTPQVRALTAASRAFFDNPPAGFCEHPLLSPRPEMVVDFSDDPEELR
RQYESGKALVPQMRLLDAEQACSIVPVLRRDKVFGATYDPTGADIDTDAL
HQGYLRGIRRNQGQVLCNHEALEIRRVDGAWEVRCDAGSYRAAVLVNAAG
AWCDAIAGLAGVRPLGLQPKRRSAFIFAPPPGIDCHDWPMLVSLDESFFL
KPDAGMLLGSPANADPVEAHDVQPEQLDIATGMYLIEEATTLTIRRPEHT
WAGLRSFVADGDLVAGYAANAEGFFWVAAQGGYGIQTSAAMGEASAALIR
HQPLPAHLREHGLDEAMLSPRRLSP
Ligand information
Ligand ID4R2
InChIInChI=1S/C32H42N12O16P2/c1-13-6-15-16(7-14(13)2)44(20(47)4-3-5-36-31(34)35)22-28(40-32(52)41-29(22)51)42(15)8-17(45)23(48)18(46)9-57-61(53,54)60-62(55,56)58-10-19-24(49)25(50)30(59-19)43-12-39-21-26(33)37-11-38-27(21)43/h3-4,6-7,11-12,17-19,23-25,30,45-46,48-50H,5,8-10H2,1-2H3,(H,53,54)(H,55,56)(H2,33,37,38)(H4,34,35,36)(H2,40,41,51,52)/b4-3+/t17-,18+,19+,23-,24+,25+,30+/m0/s1
InChIKeyUNPAMCKSCHHHHK-IGVXTPOKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc2N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C6=C(N(C(=O)C=CCNC(N)=N)c2cc1C)C(=O)NC(=O)N6
ACDLabs 12.01N=C(N)NC\C=C\C(=O)N1c2cc(C)c(C)cc2N(CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC2OC(n3cnc4c(N)ncnc43)C(O)C2O)C=2NC(=O)NC(=O)C1=2
OpenEye OEToolkits 2.0.7Cc1cc2c(cc1C)N(C3=C(N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O)NC(=O)NC3=O)C(=O)C=CCNC(=N)N
OpenEye OEToolkits 2.0.7[H]/N=C(/N)\NC/C=C/C(=O)N1c2cc(c(cc2N(C3=C1C(=O)NC(=O)N3)C[C@@H]([C@@H]([C@@H](COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O)C)C
CACTVS 3.385Cc1cc2N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)C6=C(N(C(=O)\C=C\CNC(N)=N)c2cc1C)C(=O)NC(=O)N6
FormulaC32 H42 N12 O16 P2
Name[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[5-[(~{E})-4-carbamimidamidobut-2-enoyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain7rdf Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7rdf Discovery of a new flavin N5-adduct in a tyrosine to phenylalanine variant of d-Arginine dehydrogenase.
Resolution1.29 Å
Binding residue
(original residue number in PDB)
I9 G10 G12 I13 A14 L31 E32 R33 H40 S41 T42 R44 S45 A46 H48 Y53 E87 E170 A171 A199 G200 W202 R222 F249 G303 R305 Q330 G331 G332 Y333 G334 I335 Q336
Binding residue
(residue number reindexed from 1)
I9 G10 G12 I13 A14 L31 E32 R33 H40 S41 T42 R44 S45 A46 H48 Y53 E87 E170 A171 A199 G200 W202 R222 F249 G303 R305 Q330 G331 G332 Y333 G334 I335 Q336
Annotation score1
Enzymatic activity
Enzyme Commision number 1.4.99.6: D-arginine dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008718 D-amino-acid dehydrogenase activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0006525 arginine metabolic process
GO:0006527 arginine catabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:7rdf, PDBe:7rdf, PDBj:7rdf
PDBsum7rdf
PubMed34864048
UniProtQ9HXE3|DAUA_PSEAE FAD-dependent catabolic D-arginine dehydrogenase DauA (Gene Name=dauA)

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