Structure of PDB 3imj Chain B Binding Site BS01

Receptor Information

>3imj Chain B (length=100) Species: 9606 (Homo sapiens)

KPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDV
QHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVP

Ligand information

• Ligand ID: AYI
• InChI: InChI=1S/C22H32N5O9P/c1-4-10(2)18(22(32)26-13(19(24)29)9-14(23)28)27-21(31)17-15(16(17)20(30)25-3)11-5-7-12(8-6-11)36-37(33,34)35/h5-8,10,13,15-18H,4,9H2,1-3H3,(H2,23,28)(H2,24,29)(H,25,30)(H,26,32)(H,27,31)(H2,33,34,35)/t10-,13-,15-,16+,17+,18-/m0/s1
• InChIKey: TXAWBRUKEBJWOA-LWVFFRLXSA-N
• SMILES:
  CACTVS 3.370: CC[CH](C)[CH](NC(=O)[CH]1[CH]([CH]1c2ccc(O[P](O)(O)=O)cc2)C(=O)NC)C(=O)N[CH](CC(N)=O)C(N)=O
  OpenEye OEToolkits 1.7.0: CCC(C)C(C(=O)NC(CC(=O)N)C(=O)N)NC(=O)C1C(C1C(=O)NC)c2ccc(cc2)OP(=O)(O)O
  ACDLabs 12.01: O=C(NC)C2C(c1ccc(OP(=O)(O)O)cc1)C2C(=O)NC(C(=O)NC(C(=O)N)CC(=O)N)C(C)CC
  CACTVS 3.370: CC[C@H](C)[C@H](NC(=O)[C@H]1[C@@H]([C@@H]1c2ccc(O[P](O)(O)=O)cc2)C(=O)NC)C(=O)N[C@@H](CC(N)=O)C(N)=O
  OpenEye OEToolkits 1.7.0: CC[C@H](C)[C@@H](C(=O)N[C@@H](CC(=O)N)C(=O)N)NC(=O)[C@@H]1[C@H]([C@H]1C(=O)NC)c2ccc(cc2)OP(=O)(O)O
• Formula: C22 H32 N5 O9 P
• Name: (1R,2S,3R,1S',1S")Phosphoric acid mono(4-{2-[1-(1,2-dicarbamoylethylcarbamoyl)-3-carbamoylpropylcarbamoyl]-3-methylcarbamoylcyclopropyl}phenyl) ester
• ZINC: ZINC000044670782
• PDB chain: 3imj Chain B Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3imj 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=2100000M^-1

External links

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