Structure of PDB 3imd Chain A Binding Site BS01

Receptor Information

>3imd Chain A (length=101) Species: 9606 (Homo sapiens)

MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGND
VQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQV
P

Ligand information

• Ligand ID: FYQ
• InChI: InChI=1S/C21H31N6O10P/c1-25-18(30)9-12(8-11-2-4-13(5-3-11)37-38(34,35)36)20(32)26-14(6-7-16(22)28)21(33)27-15(19(24)31)10-17(23)29/h2-5,12,14-15H,6-10H2,1H3,(H2,22,28)(H2,23,29)(H2,24,31)(H,25,30)(H,26,32)(H,27,33)(H2,34,35,36)/t12-,14+,15+/m1/s1
• InChIKey: KWOJJSIJYPOAJI-SNPRPXQTSA-N
• SMILES:
  CACTVS 3.352: CNC(=O)C[C@@H](Cc1ccc(O[P](O)(O)=O)cc1)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CC(N)=O)C(N)=O
  OpenEye OEToolkits 1.7.0: CNC(=O)C[C@@H](Cc1ccc(cc1)OP(=O)(O)O)C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H](CC(=O)N)C(=O)N
  CACTVS 3.352: CNC(=O)C[CH](Cc1ccc(O[P](O)(O)=O)cc1)C(=O)N[CH](CCC(N)=O)C(=O)N[CH](CC(N)=O)C(N)=O
  OpenEye OEToolkits 1.7.0: CNC(=O)CC(Cc1ccc(cc1)OP(=O)(O)O)C(=O)NC(CCC(=O)N)C(=O)NC(CC(=O)N)C(=O)N
• Formula: C21 H31 N6 O10 P
• Name: N~2~-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-glutaminyl-L-aspartamide
• ZINC: ZINC000044670781
• PDB chain: 3imd Chain A Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3imd Thermodynamic and Structural Effects of Conformational Constraints in Protein-Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): R67 R86 S88 S90 S96 H107 F108 K109 L120 W121
• Binding residue (residue number reindexed from 1): R13 R32 S34 S36 S42 H53 F54 K55 L66 W67
• Annotation score: 1
• Binding affinity: MOAD: Ka=560000M^-1

External links

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