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Structure of PDB 2yc0 Chain A Binding Site BS02

Receptor Information >2yc0 Chain A (length=349) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure] MAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDP RAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKF LYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTL NDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHY DEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYE RFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGA PTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN

Ligand information Ligand ID 2HG InChI InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m1/s1 InChIKey HWXBTNAVRSUOJR-GSVOUGTGSA-N SMILES Software SMILES CACTVS 3.370 O[CH](CCC(O)=O)C(O)=O ACDLabs 12.01 O=C(O)CCC(O)C(=O)O OpenEye OEToolkits 1.7.0 C(CC(=O)O)C(C(=O)O)O OpenEye OEToolkits 1.7.0 C(CC(=O)O)[C@H](C(=O)O)O CACTVS 3.370 O[C@H](CCC(O)=O)C(O)=O Formula C5 H8 O5 Name (2R)-2-hydroxypentanedioic acid ChEMBL CHEMBL1614745 DrugBank ZINC ZINC000000402968 PDB chain 2yc0 Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure Global view Local view Structure 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] PDB 2yc0 The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. Resolution 2.15 Å Binding residue (original residue number in PDB) Y145 T196 H199 N205 F207 H279 I281 W296 Binding residue (residue number reindexed from 1) Y145 T196 H199 N205 F207 H279 I281 W296 Annotation score 2 Binding affinity MOAD: ic50=1500uM PDBbind-CN: -logKd/Ki=2.82,IC50=1500uM

Enzymatic activity Enzyme Commision number 1.14.11.30: hypoxia-inducible factor-asparagine dioxygenase. 1.14.11.n4: ankyrin-repeat-histidine dioxagenase.

Gene Ontology Molecular Function GO:0003714 transcription corepressor activity GO:0005112 Notch binding GO:0005515 protein binding GO:0008198 ferrous iron binding GO:0008270 zinc ion binding GO:0019826 oxygen sensor activity GO:0031406 carboxylic acid binding GO:0036139 peptidyl-histidine dioxygenase activity GO:0036140 [protein]-asparagine 3-dioxygenase activity GO:0042803 protein homodimerization activity GO:0046872 metal ion binding GO:0051059 NF-kappaB binding GO:0051213 dioxygenase activity GO:0062101 peptidyl-aspartic acid 3-dioxygenase activity GO:0071532 ankyrin repeat binding

	Biological Process
GO:0045663	positive regulation of myoblast differentiation
GO:0045746	negative regulation of Notch signaling pathway
GO:0045892	negative regulation of DNA-templated transcription
GO:2001214	positive regulation of vasculogenesis

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0048471	perinuclear region of cytoplasm

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