Structure of PDB 8dko Chain A Binding Site BS01

Receptor Information
>8dko Chain A (length=384) Species: 707241 (Sinorhizobium meliloti SM11) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRG
KHMMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYY
RDYESAIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQAARVMGELLP
RVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLCLDGDLSGWNGMGF
VVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLDDFP
VFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFH
VGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRL
LENGANSSFVHRINDPKVSIDELIADPVEVVRAM
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain8dko Chain A Residue 2001 [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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PDB8dko Structure-based engineering of minimal proline dehydrogenase domains for inhibitor discovery.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		D306 A307 V338 Q340 R367 V369 K370 G371 A372 Y373 W374 F392 T393 R394 K395 T398 A421 T422 H423 N424 C448 L449 E492 S498 F499
Binding residue
(residue number reindexed from 1)		D169 A170 V201 Q203 R230 V232 K233 G234 A235 Y236 W237 F252 T253 R254 K255 T258 A281 T282 H283 N284 C308 L309 E352 S358 F359
Annotation score2
Enzymatic activity
Enzyme Commision number 1.2.1.88: L-glutamate gamma-semialdehyde dehydrogenase.
1.5.5.2: proline dehydrogenase.
Gene Ontology
Molecular Function
GO:0003842 1-pyrroline-5-carboxylate dehydrogenase activity
GO:0004657 proline dehydrogenase activity
Biological Process
GO:0006562 proline catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8dko, PDBe:8dko, PDBj:8dko
PDBsum8dko
PubMed36448708
UniProtF7X6I3

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