Structure of PDB 4u58 Chain A Binding Site BS01

Receptor Information

>4u58 Chain A (length=426) Species: 10090 (Mus musculus)

GTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLI
PKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLL
ASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTL
ACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADS
CWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIV
TGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQ
QVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGI
IEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLD
KIEALQRHENESVYKASLNLIEKYFS

Ligand information

• Ligand ID: 3C6
• InChI: InChI=1S/C18H22N4O2/c19-10-2-1-5-16(17(20)23)22-18(24)14-8-6-13(7-9-14)15-4-3-11-21-12-15/h3-4,6-9,11-12,16H,1-2,5,10,19H2,(H2,20,23)(H,22,24)/t16-/m0/s1
• InChIKey: VJTHQFAZPHZKKW-INIZCTEOSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: c1cc(cnc1)c2ccc(cc2)C(=O)NC(CCCCN)C(=O)N
  OpenEye OEToolkits 1.9.2: c1cc(cnc1)c2ccc(cc2)C(=O)N[C@@H](CCCCN)C(=O)N
  CACTVS 3.385: NCCCC[CH](NC(=O)c1ccc(cc1)c2cccnc2)C(N)=O
  CACTVS 3.385: NCCCC[C@H](NC(=O)c1ccc(cc1)c2cccnc2)C(N)=O
  ACDLabs 12.01: O=C(N)C(NC(=O)c2ccc(c1cccnc1)cc2)CCCCN
• Formula: C18 H22 N4 O2
• Name: N~2~-[4-(pyridin-3-yl)benzoyl]-L-lysinamide
• ZINC: ZINC000230470777
• PDB chain: 4u58 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4u58 Selective Targeting of the TPX2 Site of Importin-alpha Using Fragment-Based Ligand Design.
• Resolution: 2.56 Å
• Binding residue (original residue number in PDB): N361 A364 E396 W399 N403
• Binding residue (residue number reindexed from 1): N290 A293 E325 W328 N332
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=2.00,Kd>10.0mM

External links

• PDB: RCSB:4u58, PDBe:4u58, PDBj:4u58
• PDBsum: 4u58
• PubMed: 25899172
• UniProt: P52293|IMA1_MOUSE Importin subunit alpha-1 (Gene Name=Kpna2)