Structure of PDB 5ufi Chain B Binding Site BS01

Receptor Information

>5ufi Chain B (length=193) Species: 9606 (Homo sapiens)

SLDRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWK
FRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFY
QFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSI
PKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQI

Ligand information

• Ligand ID: 8B1
• InChI: InChI=1S/C31H47N5O4S/c1-4-28(37)33-25(19-30-34-24-11-10-23(21(2)3)18-27(24)41-30)31(39)35-26(22-8-6-5-7-9-22)20-32-29(38)12-13-36-14-16-40-17-15-36/h10-11,18,21-22,25-26H,4-9,12-17,19-20H2,1-3H3,(H,32,38)(H,33,37)(H,35,39)/t25-,26+/m0/s1
• InChIKey: CNJKDQGPBAWNRY-IZZNHLLZSA-N
• SMILES:
  CACTVS 3.385: CCC(=O)N[C@@H](Cc1sc2cc(ccc2n1)C(C)C)C(=O)N[C@H](CNC(=O)CCN3CCOCC3)C4CCCCC4
  CACTVS 3.385: CCC(=O)N[CH](Cc1sc2cc(ccc2n1)C(C)C)C(=O)N[CH](CNC(=O)CCN3CCOCC3)C4CCCCC4
  OpenEye OEToolkits 2.0.6: CCC(=O)N[C@@H](Cc1nc2ccc(cc2s1)C(C)C)C(=O)N[C@H](CNC(=O)CCN3CCOCC3)C4CCCCC4
  OpenEye OEToolkits 2.0.6: CCC(=O)NC(Cc1nc2ccc(cc2s1)C(C)C)C(=O)NC(CNC(=O)CCN3CCOCC3)C4CCCCC4
  ACDLabs 12.01: O=C(CCN1CCOCC1)NCC(NC(C(NC(CC)=O)Cc3sc2cc(C(C)C)ccc2n3)=O)C4CCCCC4
• Formula: C31 H47 N5 O4 S
• Name: N-[(1S)-1-cyclohexyl-2-{[3-(morpholin-4-yl)propanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide
• ChEMBL: CHEMBL4517307
• PDB chain: 5ufi Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ufi A potent small-molecule inhibitor of the DCN1-UBC12 interaction that selectively blocks cullin 3 neddylation.
• Resolution: 2.58 Å
• Binding residue (original residue number in PDB): I86 F89 V102 Q114 C115 E116 F117 F164 M177 Y181
• Binding residue (residue number reindexed from 1): I28 F31 V44 Q56 C57 E58 F59 F106 M119 Y123
• Annotation score: 1
• Binding affinity: BindingDB: IC50=21nM

External links

• PDB: RCSB:5ufi, PDBe:5ufi, PDBj:5ufi
• PDBsum: 5ufi
• PubMed: 29074978
• UniProt: Q96GG9|DCNL1_HUMAN DCN1-like protein 1 (Gene Name=DCUN1D1)