Structure of PDB 5yvt Chain B Binding Site BS01

Receptor Information
>5yvt Chain B (length=333) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RHTVTMIPGDGIGPELMLHVKSVFRHACVPVDFEEVHVSSNADEEDIRNA
IMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLYANVIHCKSLPG
VVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEY
AFKLAQESGRKKVTAVHKANIMKLGDGLFLQCCREVAARYPQITFENMIV
DNTTMQLVSRPQQFDVMVMPNLYGNIVNNVCAGLVGGPGLVAGANYGHVY
AVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATSIRKAVL
ASMDNENMHTPDIGGQGTTSEAIQDVIRHIRVI
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/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/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain5yvt Chain B Residue 401 [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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PDB5yvt Insights into the inhibitory mechanisms of NADH on the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		I26 E80 T81 P252 G253 R272 N273 T274 G275 S277 I278 A284 N285 D326
Binding residue
(residue number reindexed from 1)		I12 E66 T67 P238 G239 R258 N259 T260 G261 S263 I264 A270 N271 D312
Annotation score4
Binding affinityMOAD: Kd=109uM
PDBbind-CN: -logKd/Ki=3.96,Kd=109uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y135 K182 D215 N239 N243
Catalytic site (residue number reindexed from 1) Y121 K168 D201 N225 N229
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004449 isocitrate dehydrogenase (NAD+) activity
GO:0005515 protein binding
GO:0005524 ATP binding
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:0005975 carbohydrate metabolic process
GO:0006099 tricarboxylic acid cycle
GO:0006102 isocitrate metabolic process
Cellular Component
GO:0005730 nucleolus
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0045242 isocitrate dehydrogenase complex (NAD+)

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5yvt, PDBe:5yvt, PDBj:5yvt
PDBsum5yvt
PubMed29453450
UniProtP51553|IDH3G_HUMAN Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial (Gene Name=IDH3G)

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