Structure of PDB 6rb5 Chain B Binding Site BS01

Receptor Information
>6rb5 Chain B (length=489) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMSKAFDLVVIGAGSGGLEAGWNAATLYGKRVAVVDVQTSHGPPFYAALG
GTCVNVGCVPKKLMVTGAQYMDHLRESAGFGWEFDGSSVKANWKKLIAAK
NEAVLDINKSYEGMFNDTEGLDFFLGWGSLESKNVVVVRETADPKSAVKE
RLQADHILLATGSWPQMPAIPGIEHCISSNEAFYLPEPPRRVLTVGGGFI
SVEFAGIFNAYKPPGGKVTLCYRNNLILRGFDETIREEVTKQLTANGIEI
MTNENPAKVSLNTDGSKHVTFESGKTLDVDVVMMAIGRIPRTNDLQLGNV
GVKLTPKGGVQVDEFSRTNVPNIYAIGDITDRLMLTPVAINEGAALVDTV
FGNKPRKTDHTRVASAVFSIPPIGTCGLIEEVAAKEFEKVAVYMSSFTPL
MHNISGSKYKKFVAKIVTNHSDGTVLGVHLLGDGAPEIIQAVGVCLRLNA
KISDFYNTIGVHPTSAEELCSMRTPSYYYVKGEKMEKLP
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 chain6rb5 Chain B Residue 501 [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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PDB6rb5 Spiro-containing derivatives show antiparasitic activity against Trypanosoma brucei through inhibition of the trypanothione reductase enzyme.
Resolution1.977 Å
Binding residue
(original residue number in PDB)		I10 G11 G13 S14 G15 V34 D35 V36 A46 A47 G50 T51 C52 G56 C57 K60 W126 G127 T160 F198 I199 R287 R290 G326 D327 M333 L334 T335
Binding residue
(residue number reindexed from 1)		I11 G12 G14 S15 G16 V35 D36 V37 A47 A48 G51 T52 C53 G57 C58 K61 W127 G128 T161 F199 I200 R288 R291 G327 D328 M334 L335 T336
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C52 C57 K60 F198 E202 H461 E466 E485 K486
Catalytic site (residue number reindexed from 1) C53 C58 K61 F199 E203 H462 E467 E486 K487
Enzyme Commision number 1.8.1.12: trypanothione-disulfide reductase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004791 thioredoxin-disulfide reductase (NADPH) activity
GO:0015036 disulfide oxidoreductase activity
GO:0015042 trypanothione-disulfide reductase (NADPH) activity
GO:0016491 oxidoreductase activity
GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0046872 metal ion binding
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0045454 cell redox homeostasis
GO:0098869 cellular oxidant detoxification
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0020015 glycosome
GO:0097014 ciliary plasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6rb5, PDBe:6rb5, PDBj:6rb5
PDBsum6rb5
PubMed32437349
UniProtQ389T8

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