SMTL ID : 8wx7.1 (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: 4 residues within 4Å: Chain A: K.359, E.360, V.361, H.420 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.360, A:V.361, A:H.420

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 8 PLIP interactions: 8 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 pi-Cation interactions: A:R.112

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

SO4.3: 5 residues within 4Å: Chain A: E.196, K.199, P.216, Q.258, K.261 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.258 Water bridges: A:E.111, A:W.113, A:K.261 Salt bridges: A:K.199, A:K.261 SO4.4: 4 residues within 4Å: Chain A: R.139, S.141, Q.142, S.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.142, A:S.143, A:S.143 Salt bridges: A:R.139 SO4.5: 5 residues within 4Å: Chain A: K.130, K.132, Q.215, N.218, R.221 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.218 Water bridges: A:N.218, A:N.218 Salt bridges: A:K.132, A:R.221 SO4.6: 6 residues within 4Å: Chain A: Y.63, K.71, Y.280, K.365, S.366, K.367 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.63, A:S.366 Salt bridges: A:K.71, A:K.365, A:K.367 SO4.7: 5 residues within 4Å: Chain A: Y.264, S.265, R.266, K.267, Q.270 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.266, A:Q.270 Salt bridges: A:R.266, A:K.267 SO4.8: 5 residues within 4Å: Chain A: R.33, S.35, K.36, S.37, T.43 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.35, A:K.36, A:S.37 Salt bridges: A:R.33 SO4.9: 1 residues within 4Å: Chain A: R.363 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.363 SO4.10: 3 residues within 4Å: Chain A: P.425, D.426, H.427 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.426, A:H.427 SO4.11: 4 residues within 4Å: Chain A: K.370, W.372, D.374, K.379 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.379, A:K.379 Salt bridges: A:K.370, A:K.379

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
A

Tyrosine-protein phosphatase non-receptor type 11

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