Structure of PDB 3c7i Chain A Binding Site BS01

Receptor Information

>3c7i Chain A (length=101) Species: 9606 (Homo sapiens)

MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGND
VQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQV
P

Ligand information

• Ligand ID: TVN
• InChI: InChI=1S/C21H32N5O9P/c1-11(2)18(21(31)25-15(19(23)29)10-16(22)27)26-20(30)13(9-17(28)24-3)8-12-4-6-14(7-5-12)35-36(32,33)34/h4-7,11,13,15,18H,8-10H2,1-3H3,(H2,22,27)(H2,23,29)(H,24,28)(H,25,31)(H,26,30)(H2,32,33,34)/t13-,15+,18+/m1/s1
• InChIKey: CCEFGGFBPGVHRR-XUWXXGDYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)[C@@H](C(=O)N[C@@H](CC(=O)N)C(=O)N)NC(=O)[C@H](Cc1ccc(cc1)OP(=O)(O)O)CC(=O)NC
  CACTVS 3.341: CNC(=O)C[CH](Cc1ccc(O[P](O)(O)=O)cc1)C(=O)N[CH](C(C)C)C(=O)N[CH](CC(N)=O)C(N)=O
  CACTVS 3.341: CNC(=O)C[C@@H](Cc1ccc(O[P](O)(O)=O)cc1)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CC(N)=O)C(N)=O
  OpenEye OEToolkits 1.5.0: CC(C)C(C(=O)NC(CC(=O)N)C(=O)N)NC(=O)C(Cc1ccc(cc1)OP(=O)(O)O)CC(=O)NC
  ACDLabs 10.04: O=C(N)CC(C(=O)N)NC(=O)C(NC(=O)C(CC(=O)NC)Cc1ccc(OP(=O)(O)O)cc1)C(C)C
• Formula: C21 H32 N5 O9 P
• Name: N-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-valyl-L-aspartamide
• ZINC: ZINC000016052138
• PDB chain: 3c7i Chain A Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3c7i Ligand Preorganization May be Accompanied by Entropic Penalties in Protein-Ligand Interactions.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): R67 R86 S88 S90 H107 F108 K109 L120 W121
• Binding residue (residue number reindexed from 1): R13 R32 S34 S36 H53 F54 K55 L66 W67
• Annotation score: 1
• Binding affinity: MOAD: Ka=440000M^-1

External links

• PDB: RCSB:3c7i, PDBe:3c7i, PDBj:3c7i
• PDBsum: 3c7i
• PubMed: 17001728
• UniProt: P62993|GRB2_HUMAN Growth factor receptor-bound protein 2 (Gene Name=GRB2)