Structure of PDB 1xdi Chain B Binding Site BS01

Receptor Information
>1xdi Chain B (length=459) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VTRIVILGGGPAGYEAALVAATSHPETTQVTVIDCDGIGGAAVLDDCVPS
KTFIASTGLRTELRRAPHLGFHKISLPQIHARVKTLAAAQSADITAQLLS
MGVQVIAGRGELIDSTPGLARHRIKATAADGSTSEHEADVVLVATGASPR
ILPSAQPDGERILTWRQLYDLDALPDHLIVVGSGVTGAEFVDAYTELGVP
VTVVASQDHVLPYEDADAALVLEESFAERGVRLFKNARAASVTRTGAGVL
VTMTDGRTVEGSHALMTIGSVPNTSGLGLERVGIQLGRGNYLTVDRVSRT
LATGIYAAGDCTGLLPLASVAAMQGRIAMYHALGEGVSPIRLRTVAATVF
TRPEIAAVGVPQSVIDAGSVAARTIMLPLRTNARAKMSEMRHGFVKIFCR
RSTGVVIGGVVVAPIASELILPIAVAVQNRITVNELAQTLAVYPSLSGSI
TEAARRLMA
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 chain1xdi Chain B Residue 999 [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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PDB1xdi Characterization of a New Member of the Flavoprotein Disulfide Reductase Family of Enzymes from Mycobacterium tuberculosis
Resolution2.81 Å
Binding residue
(original residue number in PDB)		G9 G11 P12 A13 I34 D35 C36 D37 G41 A42 A43 D47 C48 K52 R116 G117 T152 G153 W172 T193 G316 D317 P323 L324 A325 F357
Binding residue
(residue number reindexed from 1)		G8 G10 P11 A12 I33 D34 C35 D36 G40 A41 A42 D46 C47 K51 R109 G110 T145 G146 W165 T186 G309 D310 P316 L317 A318 F350
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) A43 C48 S51 V192 E196 Y450 G455
Catalytic site (residue number reindexed from 1) A42 C47 S50 V185 E189 Y443 G448
Enzyme Commision number 1.6.5.2: NAD(P)H dehydrogenase (quinone).
Gene Ontology
Molecular Function
GO:0003955 NAD(P)H dehydrogenase (quinone) activity
GO:0008753 NADPH dehydrogenase (quinone) activity
GO:0016491 oxidoreductase activity
GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0050136 NADH:ubiquinone reductase (non-electrogenic) activity
GO:0050660 flavin adenine dinucleotide binding
GO:0070401 NADP+ binding
Biological Process
GO:1990748 cellular detoxification

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1xdi, PDBe:1xdi, PDBj:1xdi
PDBsum1xdi
PubMed15456792
UniProtP9WHH7|LPDA_MYCTU NAD(P)H dehydrogenase (quinone) (Gene Name=lpdA)

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