Structure of PDB 5zyn Chain B Binding Site BS02

Receptor Information
>5zyn Chain B (length=471) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASMKQPVVVIGSGLAGLTTSNRLISKYRIPVVLLDKAASIGGNSIKASSG
INGAHTDTQQNLKVMDTPELFLKDTLHSAKGRGVPSLMDKLTKESKSAIR
WLQTEFDLKLDLLAQLGGHSVPRTHRSSGKLPPGFEIVQALSKKLKDISS
KDSNLVQIMLNSEVVDIELDNQGHVTGVVYMDENGNRKIMKSHHVVFCSG
GFGYSKEMLKEYSPNLIHLPTTNGKQTTGDGQKILSKLGAELIDMDQVQV
HPTGFIDPNDRENNWKFLAAEALRGLGGILLHPTTGRRFTNELSTRDTVT
MEIQSKCPKNDNRALLVMSDKVYENYTNNINFYMSKNLIKKVSINDLIRQ
YDLQTTASELVTELKSYSDVNTKDTFDRPLIINAFDKDISTESTVYVGEV
TPVVHFTMGGVKINEKSQVIKKNSESVLSNGIFAAGEVSGGVHGANRLGG
SSLLECVVFGKTAADNIAKLY
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 chain5zyn Chain B Residue 604 [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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PDB5zyn Molecular basis of maintaining an oxidizing environment under anaerobiosis by soluble fumarate reductase.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		I40 G41 G43 A45 D65 K66 G72 N73 S74 A77 S78 S79 G80 V194 S229 T252 Q256 D260 L298 H435 G466 E467 G480 S482 L483 C486
Binding residue
(residue number reindexed from 1)		I10 G11 G13 A15 D35 K36 G42 N43 S44 A47 S48 S49 G50 V164 S199 T222 Q226 D230 L268 H405 G436 E437 G450 S452 L453 C456
Annotation score2
Binding affinityMOAD: Kd=4.92uM
Enzymatic activity
Catalytic site (original residue number in PDB) L146 Q279 H281 L298 E301 R304 R326 H435 F436 R477
Catalytic site (residue number reindexed from 1) L116 Q249 H251 L268 E271 R274 R296 H405 F406 R447
Enzyme Commision number 1.3.1.6: fumarate reductase (NADH).
Gene Ontology
Molecular Function
GO:0010181 FMN binding
GO:0016156 fumarate reductase (NADH) activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0034975 protein folding in endoplasmic reticulum
GO:0046443 FAD metabolic process
Cellular Component
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5zyn, PDBe:5zyn, PDBj:5zyn
PDBsum5zyn
PubMed30451826
UniProtP21375|OSM1_YEAST Fumarate reductase 2 (Gene Name=OSM1)

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