Structure of PDB 2d4v Chain A Binding Site BS02

Receptor Information
>2d4v Chain A (length=427) Species: 930 (Acidithiobacillus thiooxidans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
THIQKPATGSPLTLLNGVLQVPDQPIIPFIEGDGIGCDVTPAMRSVVDAA
VAKVYGGQRQIAWMELFAGQKAVQLYGEGQYLPDETMAAIREYKVAIKGP
LETPVGGGIRSLNVAMRQDLDLYVCLRPVRYFEGTPSPMRHPEKVDMVIF
RENSEDIYAGIEWPAGSPEAEKIIRFLREEMGVTKIRFPDSSAIGIKPVS
TEGSERLIRRTIQYALEHGKPSVSLVHKGNIMKFTEGGFRDWGYALAERE
FAGRVFTWRQKAAISKAEGKAAGQKAEQQAIADGKLIIKDVIADNFLQQI
LLRPEDYSVVATLNLNGDYVSDALAAEVGGIGMAPGANLSDTHAIFEATH
GTAPDIAGQGKANPSSLILSAVMMLEHLGWGEAAQAIVAAMNATIAAGEV
TGDLAALRGDVPALSTTEFTAALIRRF
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 chain2d4v Chain A Residue 2001 [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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PDB2d4v Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: hydride transfer and co-factor specificity
Resolution1.9 Å
Binding residue
(original residue number in PDB)		I37 P102 L103 E104 T105 N115 I333 E349 T351 H352 G353 T354 A355 D357 A364 N365 D405
Binding residue
(residue number reindexed from 1)		I35 P100 L101 E102 T103 N113 I331 E347 T349 H350 G351 T352 A353 D355 A362 N363 D403
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) Y160 K230 D296 D320 D324
Catalytic site (residue number reindexed from 1) Y158 K228 D294 D318 D322
Enzyme Commision number 1.1.1.42: isocitrate dehydrogenase (NADP(+)).
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0004450 isocitrate dehydrogenase (NADP+) activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0046872 metal ion binding
GO:0051287 NAD binding
Biological Process
GO:0006097 glyoxylate cycle
GO:0006099 tricarboxylic acid cycle

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2d4v, PDBe:2d4v, PDBj:2d4v
PDBsum2d4v
PubMed17634983
UniProtQ8GAX0

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