Structure of PDB 5a82 Chain A Binding Site BS01

Receptor Information

>5a82 Chain A (length=130) Species: 9606 (Homo sapiens)

SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQP
MDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRA
CALRDTAYAIIKEELDEDFEQLCEEIQESR

Ligand information

• Ligand ID: YEJ
• InChI: InChI=1S/C20H28N4O4S/c1-13-10-15-2-7-22-19(18(15)24-20(13)25)23-16-3-6-21-11-17(16)28-12-14-4-8-29(26,27)9-5-14/h2,7,10,14,16-17,21H,3-6,8-9,11-12H2,1H3,(H,22,23)(H,24,25)/t16-,17-/m1/s1
• InChIKey: IMRGYBMGTASFSC-IAGOWNOFSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: CC1=Cc2ccnc(c2NC1=O)NC3CCNCC3OCC4CCS(=O)(=O)CC4
  OpenEye OEToolkits 1.7.6: CC1=Cc2ccnc(c2NC1=O)N[C@@H]3CCNC[C@H]3OCC4CCS(=O)(=O)CC4
  CACTVS 3.385: CC1=Cc2ccnc(N[CH]3CCNC[CH]3OCC4CC[S](=O)(=O)CC4)c2NC1=O
  CACTVS 3.385: CC1=Cc2ccnc(N[C@@H]3CCNC[C@H]3OCC4CC[S](=O)(=O)CC4)c2NC1=O
• Formula: C20 H28 N4 O4 S
• Name: 8-[[(3R,4R)-3-[[1,1-bis(oxidanylidene)thian-4-yl]methoxy]piperidin-4-yl]amino]-3-methyl-1H-1,7-naphthyridin-2-one
• ChEMBL: CHEMBL3590396
• ZINC: ZINC000263620556
• PDB chain: 5a82 Chain A Residue 2112

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5a82 Structure-Based Optimization of Naphthyridones Into Potent Atad2 Bromodomain Inhibitors.
• Resolution: 1.86 Å
• Binding residue (original residue number in PDB): V1008 V1013 N1064 G1070 D1071 I1074 R1077
• Binding residue (residue number reindexed from 1): V30 V35 N86 G92 D93 I96 R99
• Annotation score: 1
• Binding affinity: MOAD: ic50=2.51uM
  PDBbind-CN: -logKd/Ki=5.60,IC50=2.51uM
  BindingDB: Kd=1100nM,IC50=2512nM

Enzymatic activity

• Enzyme Commision number: 3.6.1.-

External links

• PDB: RCSB:5a82, PDBe:5a82, PDBj:5a82
• PDBsum: 5a82
• PubMed: 26230603
• UniProt: Q6PL18|ATAD2_HUMAN ATPase family AAA domain-containing protein 2 (Gene Name=ATAD2)