SMTL ID : 8wx7.2 (1 other biounit)

Crystal structure of SHP2 in complex with JAB-3186

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

monomer

Ligands

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 8 residues within 4Å: Chain A: R.5, F.8, F.42, Y.64, L.75, F.252, E.253, Q.256 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.5, A:R.5, A:Y.64, A:Y.64, A:Q.256 Water bridges: A:E.253, A:E.253

1 x XD8: (5~{S})-1'-[6-azanyl-5-(2-azanyl-3-chloranyl-pyridin-4-yl)sulfanyl-pyrazin-2-yl]spiro[5,7-dihydrocyclopenta[b]pyridine-6,4'-piperidine]-5-amine(Non-covalent)

XD8.2: 17 residues within 4Å: Chain A: T.109, E.111, R.112, F.114, H.115, G.116, T.219, T.220, E.250, E.251, T.254, L.255, Q.258, D.490, P.492, K.493, Q.496 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.250, A:P.492 Hydrogen bonds: A:R.112, A:F.114, A:E.251, A:T.254, A:L.255 Water bridges: A:N.218, A:K.493 pi-Cation interactions: A:R.112

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: R.33, S.35, K.36, S.37, T.43 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.36, A:S.37, A:N.38, A:T.43 Salt bridges: A:R.33 SO4.4: 5 residues within 4Å: Chain A: Y.264, S.265, R.266, K.267, Q.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.266, A:Q.270 Salt bridges: A:R.266 SO4.5: 3 residues within 4Å: Chain A: K.199, Q.258, K.261 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.258, A:Q.258 Water bridges: A:W.113, A:K.199, A:K.199, A:K.199, A:Q.257 Salt bridges: A:K.199, A:K.261 SO4.6: 5 residues within 4Å: Chain A: R.139, S.141, Q.142, S.143, V.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.142, A:S.143 Salt bridges: A:R.139 SO4.7: 2 residues within 4Å: Chain A: R.387, E.413 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.413 Water bridges: A:E.413 Salt bridges: A:R.387 SO4.8: 3 residues within 4Å: Chain A: G.364, K.365, S.366 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.366

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

CL.9: 4 residues within 4Å: Chain A: Y.63, Y.280, K.365, K.367 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: R.221 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: K.325, K.326, H.444, Q.447 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, C. et al., Discovery of JAB-3312, a Potent SHP2 Allosteric Inhibitor for Cancer Treatment. J.Med.Chem. (2024)

Release Date

2024-08-14

Peptides

Tyrosine-protein phosphatase non-receptor type 11: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Tyrosine-protein phosphatase non-receptor type 11

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