Structure of PDB 1kdg Chain B Binding Site BS03

Receptor Information

>1kdg Chain B (length=546)

PTVSATPYDYIIVGAGPGGIIAADRLSEAGKKVLLLERGGPSTKQTGGTY
VAPWATSSGLTKFDIPGLFESLFTDSNPFWWCKDITVFAGCLVGGGTSVN
GALYWYPNDGDFSSSVGWPSSWTNHAPYTSKLSSRLPSTDHPSTDGQRYL
EQSFNVVSQLLKGQGYNQATINDNPNYKDHVFGYSAFDFLNGKRAGPVAT
YLQTALARPNFTFKTNVMVSNVVRNGSQILGVQTNDPTLGPNGFIPVTPK
GRVILSAGAFGTSRILFQSGIGPTDMIQTVQSNPTAAAALPPQNQWINLP
VGMNAQDNPSINLVFTHPSIDAYENWADVWSNPRPADAAQYLANQSGVFA
GASPKLNFWRAYSGSDGFTRYAQGTVRPGAASVNSSLPYNASQIFTITVY
LSTGIQSRGRIGIDAALRGTVLTPPWLVNPVDKTVLLQALHDVVSNIGSI
PGLTMITPDVTQTLEEYVDAYDPATMNSNHWVSSTTIGSSPQSAVVDSNV
KVFGTNNLFIVDAGIIPHLPTGNPQGTLMSAAEQAAAKILALAGGP

Ligand information

• Ligand ID: 6FA
• InChI: InChI=1S/C27H33N9O16P2/c1-9-3-11-15(18(39)10(9)2)32-17-24(33-27(44)34-25(17)43)35(11)4-12(37)19(40)13(38)5-49-53(45,46)52-54(47,48)50-6-14-20(41)21(42)26(51-14)36-8-31-16-22(28)29-7-30-23(16)36/h3,7-8,12-14,19-21,26,37-42H,4-6H2,1-2H3,(H,45,46)(H,47,48)(H2,28,29,30)(H,34,43,44)/t12-,13+,14+,19-,20+,21+,26+/m0/s1
• InChIKey: BJSUUWFQAMLNKU-OKXKTURISA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)C6=NC(=O)NC(=O)C6=Nc2c(O)c1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(c(c1C)O)N=C3C(=O)NC(=O)N=C3N2C[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
  ACDLabs 10.04: O=C2C3=Nc1c(cc(c(c1O)C)C)N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(c(c1C)O)N=C3C(=O)NC(=O)N=C3N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)C6=NC(=O)NC(=O)C6=Nc2c(O)c1C
• Formula: C27 H33 N9 O16 P2
• Name: 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE
• DrugBank: DB02654
• ZINC: ZINC000085587514
• PDB chain: 1kdg Chain B Residue 7801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1kdg Crystal Structure of the Flavoprotein Domain of the Extracellular Flavocytochrome Cellobiose Dehydrogenase
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): V222 G223 P226 E246 R247 G299 C300 G304 G305 N309 G310 L312 M427 V428 A466 G467 N688 H689 D721 A722 N732 Q734 L737
• Binding residue (residue number reindexed from 1): V13 G14 P17 E37 R38 G90 C91 G95 G96 N100 G101 L103 M218 V219 A257 G258 N479 H480 D512 A513 N523 Q525 L528
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y609 H689 N732
• Catalytic site (residue number reindexed from 1): Y400 H480 N523
• Enzyme Commision number: 1.1.99.18: cellobiose dehydrogenase (acceptor).

Gene Ontology

Molecular Function

• GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
• GO:0050660 flavin adenine dinucleotide binding

External links

• PDB: RCSB:1kdg, PDBe:1kdg, PDBj:1kdg
• PDBsum: 1kdg
• PubMed: 11786022
• UniProt: Q01738|CDH_PHACH Cellobiose dehydrogenase (Gene Name=CDH-1)