Structure of PDB 3in7 Chain A Binding Site BS01

Receptor Information

>3in7 Chain A (length=99) Species: 9606 (Homo sapiens)

MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGND
VQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQ

Ligand information

• Ligand ID: AYQ
• InChI: InChI=1S/C21H29N6O10P/c1-25-20(32)16-15(9-2-4-10(5-3-9)37-38(34,35)36)17(16)21(33)26-11(6-7-13(22)28)19(31)27-12(18(24)30)8-14(23)29/h2-5,11-12,15-17H,6-8H2,1H3,(H2,22,28)(H2,23,29)(H2,24,30)(H,25,32)(H,26,33)(H,27,31)(H2,34,35,36)/t11-,12-,15-,16+,17+/m0/s1
• InChIKey: RYXSIJXAOLAGQV-PASATYPHSA-N
• SMILES:
  CACTVS 3.370: CNC(=O)[C@H]1[C@@H]([C@H]1c2ccc(O[P](O)(O)=O)cc2)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)C1C(C1C(=O)NC(CCC(=O)N)C(=O)NC(CC(=O)N)C(=O)N)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)CCC(=O)N
  OpenEye OEToolkits 1.7.0: CNC(=O)[C@@H]1[C@@H]([C@H]1C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H](CC(=O)N)C(=O)N)c2ccc(cc2)OP(=O)(O)O
  CACTVS 3.370: CNC(=O)[CH]1[CH]([CH]1c2ccc(O[P](O)(O)=O)cc2)C(=O)N[CH](CCC(N)=O)C(=O)N[CH](CC(N)=O)C(N)=O
• Formula: C21 H29 N6 O10 P
• Name: N~2~-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-D-glutaminyl-D-aspartamide
• ZINC: ZINC000058661078
• PDB chain: 3in7 Chain A Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3in7 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 Q106 H107 F108 K109 L120 W121
• Binding residue (residue number reindexed from 1): R13 R32 S34 S36 S42 Q52 H53 F54 K55 L66 W67
• Annotation score: 1
• Binding affinity: MOAD: Ka=1200000M^-1

External links

• PDB: RCSB:3in7, PDBe:3in7, PDBj:3in7
• PDBsum: 3in7
• PubMed: 19886660
• UniProt: P62993|GRB2_HUMAN Growth factor receptor-bound protein 2 (Gene Name=GRB2)