SMTL ID : 3n84.1 (8 other biounits)

Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x PTR- VAL- ASN- VAL- PRO- 011: 23-membered peptide-like macrocyclic ligand(Non-covalent)

PTR-VAL-ASN-VAL-PRO-011.1: 14 residues within 4Å: Chain A: R.16, R.35, S.37, S.39, S.45, Q.55, H.56, F.57, K.58, L.60, L.69, W.70, S.90, N.92 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Q.55, A:H.56, A:F.57, A:F.57, A:L.60 Hydrogen bonds: A:R.16, A:R.16, A:S.37, A:S.39, A:S.39, A:S.45, A:S.45, A:H.56, A:K.58, A:L.69, A:N.92 Water bridges: A:S.39, A:S.39, A:K.58, A:K.58 Salt bridges: A:R.16, A:R.35, A:K.58 pi-Cation interactions: A:R.16 PTR-VAL-ASN-VAL-PRO-011.2: 14 residues within 4Å: Chain B: R.16, R.35, S.37, S.39, S.45, Q.55, H.56, F.57, K.58, L.69, W.70, S.90, N.92 Ligands: GOL.6 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:Q.55, B:H.56, B:F.57, B:F.57, B:K.58 Hydrogen bonds: B:R.16, B:R.16, B:S.37, B:S.39, B:S.39, B:S.45, B:H.56, B:K.58, B:L.69 Water bridges: B:S.39, B:S.39, B:K.58, B:N.92 Salt bridges: B:R.16, B:R.35 pi-Cation interactions: B:R.16

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: W.70, V.71, V.72, R.91 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: T.87, S.88, S.90 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: F.44, R.61, Y.67 Chain B: G.42, F.44, V.59, R.61 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:F.44, B:V.59, B:R.61, B:R.61, A:R.61, A:R.61, A:Y.67, A:Y.67 GOL.6: 4 residues within 4Å: Chain B: R.16, S.39 Ligands: PTR-VAL-ASN-VAL-PRO-011.2, PTR-VAL-ASN-VAL-PRO-011.2 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delorbe, J.E. et al., Thermodynamic and Structural Effects of Macrocyclization as a Constraining Method in Protein-Ligand Interactions. ACS MED.CHEM.LETT. (2010)

Release Date

2011-01-12

Peptides

Growth factor receptor-bound protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Growth factor receptor-bound protein 2

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