Structure of PDB 6lum Chain J Binding Site BS01

Receptor Information
>6lum Chain J (length=534) Species: 1445611 (Mycolicibacterium smegmatis MC2 51) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IQEHRYDVVIVGAGGAGMRAAVEAGPRARTAVLTKLYPTRSHTGAAQGGM
CAALANVEEDNWEWHTFDTVKGGDYLADQDAVEIMCKEAIDAVLDLEKMG
MPFNRTPEGRIDQRRFGGHTRDHGKAPVRRACYAADRTGHMILQTLYQNC
VKHDVEFFNEFYALDIALTETPAGPVATGVIAYELATGDIHVFHAKAIVF
ATGGSGRMYKTTSNAHTLTGDGLGIVFRKGLPLEDMEFHQFHPTGLAGLG
ILISEAVRGEGGRLLNGEGERFMERYAPTIVDLAPRDIVARSMVLEVLEV
PVYPTCHYVMGGIPTTVNGQVLRDNTNVIPGLYAAGECACVSVHGANRLG
TNSLLDINVFGRRAGIAAAEYAQNHNFVDMPENPAEMVVGWVGDILSEHG
NERVADIRGALQQSMDNNAAVFRTEETLKQALTDIHALKERYSRITVHDK
GKRYNSDLLEAIELGFLLELAEVTVVGALNRKESRGGHAREDYPNRDDTN
YMRHTMAYKQGTDLLSDIRLDYKPVVQTRYEPME
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 chain6lum Chain J Residue 700 [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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PDB6lum Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF.
Resolution2.84 Å
Binding residue
(original residue number in PDB)		G13 A17 K36 S42 H43 T44 A46 A47 G49 A164 T203 G204 S214 D222 H354 E384 R395 T398 S400
Binding residue
(residue number reindexed from 1)		G12 A16 K35 S41 H42 T43 A45 A46 G48 A163 T202 G203 S213 D221 H307 E337 R348 T351 S353
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) F117 Q241 H243 L253 E256 R259 R287 H354 Y355 R395
Catalytic site (residue number reindexed from 1) F116 Q240 H242 L252 E255 R258 R286 H307 Y308 R348
Enzyme Commision number 1.3.5.1: succinate dehydrogenase.
Gene Ontology
Molecular Function
GO:0000104 succinate dehydrogenase activity
GO:0008177 succinate dehydrogenase (quinone) activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0033765 steroid dehydrogenase activity, acting on the CH-CH group of donors
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0006099 tricarboxylic acid cycle
GO:0008202 steroid metabolic process
GO:0009061 anaerobic respiration
GO:0022900 electron transport chain
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6lum, PDBe:6lum, PDBj:6lum
PDBsum6lum
PubMed32843629
UniProtA0QT08

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