Structure of PDB 3kfj Chain A Binding Site BS01

Receptor Information

>3kfj Chain A (length=100) Species: 9606 (Homo sapiens)

KPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDV
QHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVP

Ligand information

• Ligand ID: YEN
• InChI: InChI=1S/C21H30N5O11P/c1-24-17(28)9-12(8-11-2-4-13(5-3-11)37-38(34,35)36)20(32)25-14(6-7-18(29)30)21(33)26-15(19(23)31)10-16(22)27/h2-5,12,14-15H,6-10H2,1H3,(H2,22,27)(H2,23,31)(H,24,28)(H,25,32)(H,26,33)(H,29,30)(H2,34,35,36)/t12-,14-,15-/m0/s1
• InChIKey: NPYWTYXAKSZNLF-QEJZJMRPSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CNC(=O)C[C@H](Cc1ccc(cc1)OP(=O)(O)O)C(=O)N[C@@H](CCC(=O)O)C(=O)N[C@@H](CC(=O)N)C(=O)N
  OpenEye OEToolkits 1.7.0: CNC(=O)CC(Cc1ccc(cc1)OP(=O)(O)O)C(=O)NC(CCC(=O)O)C(=O)NC(CC(=O)N)C(=O)N
  CACTVS 3.370: CNC(=O)C[CH](Cc1ccc(O[P](O)(O)=O)cc1)C(=O)N[CH](CCC(O)=O)C(=O)N[CH](CC(N)=O)C(N)=O
  CACTVS 3.370: CNC(=O)C[C@H](Cc1ccc(O[P](O)(O)=O)cc1)C(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](CC(N)=O)C(N)=O
  ACDLabs 12.01: O=C(N)C(NC(=O)C(NC(=O)C(CC(=O)NC)Cc1ccc(OP(=O)(O)O)cc1)CCC(=O)O)CC(=O)N
• Formula: C21 H30 N5 O11 P
• Name: N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-alpha-glutamyl-L-aspartamide
• ZINC: ZINC000098209636
• PDB chain: 3kfj Chain A Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3kfj Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization.
• Resolution: 2.02 Å
• Binding residue (original residue number in PDB): R67 R86 S88 S90 S96 Q106 H107 F108 K109 L120 W121
• Binding residue (residue number reindexed from 1): R12 R31 S33 S35 S41 Q51 H52 F53 K54 L65 W66
• Annotation score: 1
• Binding affinity: MOAD: Ka=300000M^-1

External links

• PDB: RCSB:3kfj, PDBe:3kfj, PDBj:3kfj
• PDBsum: 3kfj
• PubMed: 19886660
• UniProt: P62993|GRB2_HUMAN Growth factor receptor-bound protein 2 (Gene Name=GRB2)