SMTL ID : 5vfi.1

Bruton's tyrosine kinase (BTK) with GDC-0853

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

1 x 9AJ: 2-[3'-(hydroxymethyl)-1-methyl-5-({5-[(2S)-2-methyl-4-(oxetan-3-yl)piperazin-1-yl]pyridin-2-yl}amino)-6-oxo[1,6-dihydro[3,4'-bipyridine]]-2'-yl]-7,7-dimethyl-3,4,7,8-tetrahydro-2H-cyclopenta[4,5]pyrrolo[1,2-a]pyrazin-1(6H)-one(Non-covalent)

9AJ.1: 23 residues within 4Å: Chain A: L.20, G.21, T.22, G.23, Q.24, F.25, V.28, A.40, K.42, T.86, E.87, Y.88, M.89, A.90, N.91, G.92, D.133, N.138, L.140, S.150, D.151, S.155, Y.163 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.20, A:F.25, A:F.25, A:V.28, A:Y.88, A:L.140, A:D.151, A:Y.163 Hydrogen bonds: A:K.42, A:M.89, A:M.89, A:S.150, A:S.150 Water bridges: A:G.23, A:C.93

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

EDO.2: 9 residues within 4Å: Chain A: R.132, D.133, L.134, P.172, W.175, S.176, V.180, F.186, A.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.134, A:L.134 EDO.3: 4 residues within 4Å: Chain A: R.104, F.105, L.205, L.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.105 Water bridges: A:F.105 EDO.4: 3 residues within 4Å: Chain A: S.187, S.188, K.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.188, A:K.189 Water bridges: A:S.187 EDO.5: 5 residues within 4Å: Chain A: Y.88, M.89, A.90, N.142, D.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.90, A:D.143 EDO.6: 3 residues within 4Å: Chain A: T.107, S.235, E.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.107, A:T.107 Water bridges: A:S.235 EDO.7: 2 residues within 4Å: Chain A: T.15, F.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.16, A:F.16 EDO.8: 2 residues within 4Å: Chain A: Q.106, Q.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.109, A:Q.109 EDO.9: 4 residues within 4Å: Chain A: Y.210, E.211, R.212, F.213 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.210, A:R.212 Water bridges: A:Y.210, A:Y.210, A:E.211

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

SO4.10: 2 residues within 4Å: Chain A: G.1, R.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.1 Water bridges: A:R.34 Salt bridges: A:R.34 SO4.11: 4 residues within 4Å: Chain A: S.204, K.207, P.231, H.232 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.232 Water bridges: A:K.207, A:H.232, A:L.233 Salt bridges: A:K.207, A:H.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crawford, J.J. et al., Discovery of GDC-0853: A Potent, Selective, and Noncovalent Bruton's Tyrosine Kinase Inhibitor in Early Clinical Development. J. Med. Chem. (2018)

Release Date

2018-02-28

Peptides

Tyrosine-protein kinase BTK: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrosine-protein kinase BTK

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