Structure of PDB 5grf Chain B Binding Site BS01
Receptor Information
>5grf Chain B (length=335) Species:
9606
(Homo sapiens) [
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RHTVTMIPGDGIGPELMLHVKSVFRHACVPVDFEEVHVSSNADEEDIRNA
IMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLDLYANVIHCKSLPG
VVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLAIITKAKSLRIAEY
AFKLAQESGRKKVTAVHKANIMKLGDGLFLQCCREVAARYPQITFENMIV
DNTTMQLVSRPQQFDVMVMPNLYGNIVNNVCAGLVGGPGLVAGANYGHVY
AVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATSIRKAVL
ASMDNENMHTPDIGGQGTTSEAIQDVIRHIRVING
Ligand information
Ligand ID
ADP
InChI
InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKey
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341
Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04
O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341
Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Formula
C10 H15 N5 O10 P2
Name
ADENOSINE-5'-DIPHOSPHATE
ChEMBL
CHEMBL14830
DrugBank
DB16833
ZINC
ZINC000012360703
PDB chain
5grf Chain B Residue 402 [
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Receptor-Ligand Complex Structure
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PDB
5grf
Molecular mechanism of the allosteric regulation of the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase.
Resolution
2.5 Å
Binding residue
(original residue number in PDB)
I26 P252 N273 T274 G275 K276 I278 N285 D326
Binding residue
(residue number reindexed from 1)
I12 P238 N259 T260 G261 K262 I264 N271 D312
Annotation score
3
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
1.1.1.41
: isocitrate dehydrogenase (NAD(+)).
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+)
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Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:5grf
,
PDBe:5grf
,
PDBj:5grf
PDBsum
5grf
PubMed
28098230
UniProt
P51553
|IDH3G_HUMAN Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial (Gene Name=IDH3G)
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