Structure of PDB 2gh5 Chain B Binding Site BS02

Receptor Information

>2gh5 Chain B (length=461) Species: 9606 (Homo sapiens)

VASYDYLVIGGGSGGLASARRAAELGARAAVVESHKLGGTCVNVGCVPKK
VMWNTAVHSEFMHDHADYGFPSCEGKFNWRVIKEKRDAYVSRLNAIYQNN
LTKSHIEIIRGHAAFTSDPKPTIEVSGKKYTAPHILIATGGMPSTPHESQ
IPGASLGITSDGFFQLEELPGRSVIVGAGYIAVEMAGILSALGSKTSLMI
RHDKVLRSFDSMISTNCTEELENAGVEVLKFSQVKEVKKTLSGLEVSMVT
AVPGRLPVMTMIPDVDCLLWAIGRVPNTKDLSLNKLGIQTDDKGHIIVDE
FQNTNVKGIYAVGDVCGKALLTPVAIAAGRKLAHRLFEYKEDSKLDYNNI
PTVVFSHPPIGTVGLTEDEAIHKYGIENVKTYSTSFTPMYHAVTKRKTKC
VMKMVCANKEEKVVGIHMQGLGCDEMLQGFAVAVKMGATKADFDNTVAIH
PTSSEELVTLR

Ligand information

• Ligand ID: FAD
• InChI: InChI=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
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=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 1.5.0: Cc1cc2c(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 1.5.0: Cc1cc2c(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 3.341: Cc1cc2N=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 10.04: O=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
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 2gh5 Chain B Residue 479

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2gh5 A fluoro analogue of the menadione derivative 6-[2'-(3'-methyl)-1',4'-naphthoquinolyl]hexanoic acid is a suicide substrate of glutathione reductase. Crystal structure of the alkylated human enzyme
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): G29 S30 G31 V49 E50 S51 H52 G56 T57 G62 C63 K66 H129 A130 T156 G157 Y197 I198 R291 G330 D331 L337 L338 T339
• Binding residue (residue number reindexed from 1): G12 S13 G14 V32 E33 S34 H35 G39 T40 G45 C46 K49 H112 A113 T139 G140 Y180 I181 R274 G313 D314 L320 L321 T322
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): L54 C58 C63 K66 Y197 E201 A465 H467 E472
• Catalytic site (residue number reindexed from 1): L37 C41 C46 K49 Y180 E184 A448 H450 E455
• Enzyme Commision number: 1.8.1.7: glutathione-disulfide reductase.

Gene Ontology

Molecular Function

• GO:0004362 glutathione-disulfide reductase (NADPH) activity
• GO:0009055 electron transfer activity
• GO:0016491 oxidoreductase activity
• GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
• GO:0050660 flavin adenine dinucleotide binding
• GO:0050661 NADP binding

Biological Process

• GO:0006749 glutathione metabolic process
• GO:0034599 cellular response to oxidative stress
• GO:0045454 cell redox homeostasis
• GO:0098869 cellular oxidant detoxification

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0005829 cytosol
• GO:0009897 external side of plasma membrane
• GO:0070062 extracellular exosome

External links

• PDB: RCSB:2gh5, PDBe:2gh5, PDBj:2gh5
• PDBsum: 2gh5
• PubMed: 16910673
• UniProt: P00390|GSHR_HUMAN Glutathione reductase, mitochondrial (Gene Name=GSR)