SMTL ID : 8u2d.1

Bruton's tyrosine kinase in complex with N-[(2R)-1-[(3R)-3-(methylcarbamoyl)-1H,2H,3H,4H,9H-pyrido[3,4-b]indol-2-yl]-3-(3-methylphenyl)-1-oxopropan-2-yl]-1H-indazole-5-carboxamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x UQX: (3R)-2-[N-(1H-indazole-5-carbonyl)-3-methyl-D-phenylalanyl]-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide(Non-covalent)

UQX.1: 24 residues within 4Å: Chain A: L.20, G.21, T.22, G.23, Q.24, F.25, G.26, V.27, V.28, A.40, K.42, M.43, I.44, I.84, E.87, Y.88, M.89, G.92, C.93, R.137, N.138, L.140, D.151, L.154 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.20, A:F.25, A:V.28, A:K.42, A:I.44, A:I.84, A:R.137, A:L.140, A:L.140, A:L.154 Hydrogen bonds: A:T.22, A:F.25, A:G.26, A:K.42, A:M.89, A:M.89, A:D.151 Water bridges: A:S.150 pi-Stacking: A:F.25

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: E.211, R.212, F.213 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.212 Water bridges: A:Y.210

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

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

SO4.4: 6 residues within 4Å: Chain A: F.171, P.172, V.173, R.174, W.175, N.215 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.173, A:R.174, A:N.215 Water bridges: A:F.171 Salt bridges: A:R.174 SO4.5: 7 residues within 4Å: Chain A: Y.210, F.213, L.226, R.227, L.228, Y.229 Ligands: NA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.229 Water bridges: A:Y.210, A:E.211

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

EDO.6: 2 residues within 4Å: Chain A: Q.79, R.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.80, A:R.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robbins, D.W. et al., Discovery and Preclinical Pharmacology of NX-2127, an Orally Bioavailable Degrader of Bruton's Tyrosine Kinase with Immunomodulatory Activity for the Treatment of Patients with B Cell Malignancies. J.Med.Chem. (2024)

Release Date

2024-01-31

Peptides

Tyrosine-protein kinase BTK: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrosine-protein kinase BTK

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