Structure of PDB 5dn9 Chain B Binding Site BS01

Receptor Information
>5dn9 Chain B (length=361) Species: 5477 ([Candida] boidinii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKIVLVLYDAGKHAADEEKLYGCTENKLGIANWLKDQGHELITTSDKEGG
NSVLDQHIPDADIIITTPFHPAYITKERIDKAKKLKLVVVAGVGSDHIDL
DYINQTGKKISVLEVTGSNVVSVAEHVLMTMLVLVRNFVPAHEQIINHDW
EVAAIAKDAYDIEGKTIATIGAGRIGYRVLERLVPFNPKELLYYDYQALP
KDAEEKVGARRVENIEELVAQADIVTINAPLHAGTKGLINKELLSKFKKG
AWLVNTARGAICVAEDVAAALESGQLRGYGGDVWFPQPAPKDHPWRDMRN
KYGAGNAMTPHYSGTTLDAQTRYAEGTKNILESFFTGKFDYRPQDIILLN
GEYITKAYGKH
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain5dn9 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5dn9 Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		V93 N119 V123 R174 I175 Y194 D195 Y196 A229 P230 H232 T235 T256 A257 R258 D282 H311 S313 G314 A357
Binding residue
(residue number reindexed from 1)		V93 N119 V123 R174 I175 Y194 D195 Y196 A229 P230 H232 T235 T256 A257 R258 D282 H311 S313 G314 A357
Annotation score4
Binding affinityMOAD: Kd=92uM
Enzymatic activity
Catalytic site (original residue number in PDB) N119 R258 D282 Q287 H311
Catalytic site (residue number reindexed from 1) N119 R258 D282 Q287 H311
Enzyme Commision number 1.17.1.9: formate dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008863 formate dehydrogenase (NAD+) activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding
Biological Process
GO:0019752 carboxylic acid metabolic process
GO:0042183 formate catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5dn9, PDBe:5dn9, PDBj:5dn9
PDBsum5dn9
PubMed27100912
UniProtA0A0A1EQY0

[Back to BioLiP]