Structure of PDB 4u5v Chain A Binding Site BS01

Receptor Information

>4u5v Chain A (length=426) Species: 10090 (Mus musculus)

GTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLI
PKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLL
ASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTL
ACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADS
CWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIV
TGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQ
QVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGI
IEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLD
KIEALQRHENESVYKASLNLIEKYFS

Ligand information

• Ligand ID: RH2
• InChI: InChI=1S/C16H22N4OS/c17-8-2-1-5-14(16(18)21)20-11-13-6-7-15(22-13)12-4-3-9-19-10-12/h3-4,6-7,9-10,14,20H,1-2,5,8,11,17H2,(H2,18,21)/t14-/m0/s1
• InChIKey: KBSBPTGVGQZWKP-AWEZNQCLSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: c1cc(cnc1)c2ccc(s2)CNC(CCCCN)C(=O)N
  CACTVS 3.385: NCCCC[C@H](NCc1sc(cc1)c2cccnc2)C(N)=O
  OpenEye OEToolkits 1.9.2: c1cc(cnc1)c2ccc(s2)CN[C@@H](CCCCN)C(=O)N
  CACTVS 3.385: NCCCC[CH](NCc1sc(cc1)c2cccnc2)C(N)=O
  ACDLabs 12.01: NC(C(NCc1sc(cc1)c2cccnc2)CCCCN)=O
• Formula: C16 H22 N4 O S
• Name: N~2~-{[5-(pyridin-3-yl)thiophen-2-yl]methyl}-L-lysinamide
• ZINC: ZINC000263620638
• PDB chain: 4u5v Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4u5v Selective Targeting of the TPX2 Site of Importin-alpha Using Fragment-Based Ligand Design.
• Resolution: 1.968 Å
• Binding residue (original residue number in PDB): N361 E396 W399 N403
• Binding residue (residue number reindexed from 1): N290 E325 W328 N332
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.9mM
  PDBbind-CN: -logKd/Ki=3.05,Kd=0.9mM

External links

• PDB: RCSB:4u5v, PDBe:4u5v, PDBj:4u5v
• PDBsum: 4u5v
• PubMed: 25899172
• UniProt: P52293|IMA1_MOUSE Importin subunit alpha-1 (Gene Name=Kpna2)