Structure of PDB 3in8 Chain A Binding Site BS01

Receptor Information

>3in8 Chain A (length=101) Species: 9606 (Homo sapiens)

MKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGND
VQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQV
P

Ligand information

• Ligand ID: FYI
• InChI: InChI=1S/C22H34N5O9P/c1-4-12(2)19(22(32)26-16(20(24)30)11-17(23)28)27-21(31)14(10-18(29)25-3)9-13-5-7-15(8-6-13)36-37(33,34)35/h5-8,12,14,16,19H,4,9-11H2,1-3H3,(H2,23,28)(H2,24,30)(H,25,29)(H,26,32)(H,27,31)(H2,33,34,35)/t12-,14-,16-,19-/m0/s1
• InChIKey: UEYBGJJDTRNDGF-HAHWVIBASA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CCC(C)C(C(=O)NC(CC(=O)N)C(=O)N)NC(=O)C(Cc1ccc(cc1)OP(=O)(O)O)CC(=O)NC
  CACTVS 3.370: CC[C@H](C)[C@H](NC(=O)[C@H](CC(=O)NC)Cc1ccc(O[P](O)(O)=O)cc1)C(=O)N[C@@H](CC(N)=O)C(N)=O
  CACTVS 3.370: CC[CH](C)[CH](NC(=O)[CH](CC(=O)NC)Cc1ccc(O[P](O)(O)=O)cc1)C(=O)N[CH](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](Cc1ccc(cc1)OP(=O)(O)O)CC(=O)NC
  ACDLabs 12.01: O=C(N)C(NC(=O)C(NC(=O)C(CC(=O)NC)Cc1ccc(OP(=O)(O)O)cc1)C(C)CC)CC(=O)N
• Formula: C22 H34 N5 O9 P
• Name: N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-isoleucyl-L-aspartamide
• ZINC: ZINC000098208910
• PDB chain: 3in8 Chain A Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3in8 Thermodynamic and Structural Effects of Conformational Constraints in Protein-Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization.
• Resolution: 1.7 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=400000M^-1

External links

• PDB: RCSB:3in8, PDBe:3in8, PDBj:3in8
• PDBsum: 3in8
• PubMed: 19886660
• UniProt: P62993|GRB2_HUMAN Growth factor receptor-bound protein 2 (Gene Name=GRB2)