Structure of PDB 7my9 Chain B Binding Site BS02

Receptor Information
>7my9 Chain B (length=1216) Species: 707241 (Sinorhizobium meliloti SM11) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APAPFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDA
AASTARKLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPD
TATRDALIRDKIADGNWKSHRSLFVNAATWGLVVTGKLTSTVNDRSLAAA
LTRLISRCGEPVIRRGVDMAMRMMGEQFVTGETIREALKRSKELEEKGFS
YSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISIKLS
ALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSL
DLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVR
LVKGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVF
PQFATHNAQTLAAIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLD
RPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRINDPKVSIDELIADP
VEVVRAMPVVGAKHDRIALPAELFGDARTNSAGLDLSNEETLASLTEALR
ESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETSEEDARRAV
RLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALN
AIAEVREAIDFLRYYAEQTRRTLGPGHGPLGPIVCISPWNFPLAIFTGQI
AAALVAGNPVLAKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRVGA
ALVAAAETAGVMFTGSTEVARLIQAQLADRLSPAGRPIPLIAETGGQNAM
IVDSSALAEQVVGDVITSAFDSAGQRCSALRVLCLQEDVADRILTMLKGA
LHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRKVEQIGLASE
TGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATG
YGLTFGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSG
TGPKAGGPLYLGRLVTTAPVPPQHSSVHTDPVLLDFAKWLDGKGARAEAE
AARNAGSSSALGLDLELPGPVGERNLYTLHARGRILLVPATESGLYHQLA
AALATGNSVAIDAASGLQASLKNLPQTVGLRVSWSKDWAADGPFAGALVE
GDAERIRAVNKAIAALPGPLLLVQAASSGEIARNPDAYCLNWLVEEVSAS
INTAAAGGNASLMAIG
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 chain7my9 Chain B Residue 1303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7my9 Photoinduced Covalent Irreversible Inactivation of Proline Dehydrogenase by S-Heterocycles.
Resolution1.628 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)
D289 A290 V321 Q323 R350 V352 K353 G354 A355 Y356 W357 F375 T376 R377 K378 T381 A404 T405 H406 N407 C431 L432 E475 S481 F482
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:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003700 DNA-binding transcription factor activity
GO:0003842 1-pyrroline-5-carboxylate dehydrogenase activity
GO:0004657 proline dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0006560 proline metabolic process
GO:0006561 proline biosynthetic process
GO:0006562 proline catabolic process
GO:0010133 proline catabolic process to glutamate
Cellular Component
GO:0009898 cytoplasmic side of plasma membrane

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:7my9, PDBe:7my9, PDBj:7my9
PDBsum7my9
PubMed34542291
UniProtF7X6I3

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