Structure of PDB 7d6x Chain A Binding Site BS01

Receptor Information
>7d6x Chain A (length=594) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LERHSYDVVVIGAGGAGLRAVIEARERGLRVAVVTKSLFGKAHTVMAEGG
CAAAMRNVNTKDSWQVHFGDTMRGGKFLNNWRMAELHAQEAPDRVWELET
YGALFDRTKDGKISQRNFGGHTYPRLAHVGDRTGLEIIRTLQQKIVSLQQ
EDKRELGDYEARIRVFHETSITELILDDGKIAGAFGYYRETGNFVLFEAP
AVVLATGGIGKSFKVSSNSWEYTGDGHALALRAGSALINMEFIQFHPTGM
VWPLSVKGILVTEGVRGDGGVLKNSEGKTPDLLPRDEVARAINAEVKAGR
GSPHGGVYLDIASRMPAEEIKRRLPSMYHQFIELAEVDITKDAMEVGPTC
HYVMGGIEVDPDTAAGATPGLFAAGECSGGMHGSNRLGGNSLSDLLVFGR
RAGLGAADYVRALPDRPKVSEAAVEDATRLVLAPFEPKAEPENPYTLHAE
LQQSMNDLVGIIRKEAEIQEALDRLQELKRRYANVTVEGGRVFNPGWHLA
IDMRNMLLVSECVAKAALQRTESRGGHTRDDYPEMDANWRNTLLVCRVSG
GDPVVPDVTVTPEQQVPMRPDLLGCFELSELEKYYTPEELAEHP
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 chain7d6x Chain A Residue 701 [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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PDB7d6x Architecture of the mycobacterial succinate dehydrogenase with a membrane-embedded Rieske FeS cluster.
Resolution2.88 Å
Binding residue
(original residue number in PDB)		I14 G15 K39 A45 H46 T47 A50 E51 G52 I174 T209 S220 E224 Y225 H388 Y389 E413 R423 G426 S428 L429 L432
Binding residue
(residue number reindexed from 1)		I11 G12 K36 A42 H43 T44 A47 E48 G49 I171 T206 S217 E221 Y222 H351 Y352 E376 R386 G389 S391 L392 L395
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) F121 Q247 H249 L263 E266 R269 R322 H388 Y389 R423
Catalytic site (residue number reindexed from 1) F118 Q244 H246 L260 E263 R266 R285 H351 Y352 R386
Enzyme Commision number 1.3.99.1: Deleted entry.
Gene Ontology
Molecular Function
GO:0000104 succinate dehydrogenase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0033765 steroid dehydrogenase activity, acting on the CH-CH group of donors
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0008202 steroid metabolic process
GO:0009061 anaerobic respiration
Cellular Component
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7d6x, PDBe:7d6x, PDBj:7d6x
PDBsum7d6x
PubMed33876763
UniProtA0QPJ3

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