SMTL ID : 6fex.1

DDR1, 2-[4-bromo-2-oxo-1'-(1H-pyrazolo[4,3-b]pyridine-5-carbonyl)spiro[indole-3,4'-piperidine]-1-yl]-N-(2,2,2-trifluoroethyl)acetamide, 1.291A, P212121, Rfree=17.4%

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

monomer

Ligands

1 x D6Z: 2-[4-bromanyl-2-oxidanylidene-1'-(1~{H}-pyrazolo[4,3-b]pyridin-5-ylcarbonyl)spiro[indole-3,4'-piperidine]-1-yl]-~{N}-[2,2,2-tris(fluoranyl)ethyl]ethanamide(Non-covalent)

D6Z.1: 25 residues within 4Å: Chain A: L.24, G.25, V.32, A.61, K.63, E.80, M.84, L.87, I.92, I.93, L.95, M.107, T.109, D.110, Y.111, M.112, G.115, L.159, F.164, H.166, L.175, I.184, A.185, D.186, F.187 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.32, A:K.63, A:M.107, A:F.187 Hydrogen bonds: A:M.112, A:M.112, A:D.186 Water bridges: A:E.80, A:G.115 pi-Cation interactions: A:K.63

4 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 6 residues within 4Å: Chain A: L.285, R.288, P.298, Q.302, L.303, F.306 Ligand excluded by PLIP IOD.3: 5 residues within 4Å: Chain A: G.27, G.30, E.31, V.32, K.63 Ligand excluded by PLIP IOD.4: 4 residues within 4Å: Chain A: F.29, R.66, A.69, T.70 Ligand excluded by PLIP IOD.5: 5 residues within 4Å: Chain A: F.247, G.248, Q.249, L.250 Ligands: MES.6 Ligand excluded by PLIP

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 11 residues within 4Å: Chain A: W.236, M.240, A.244, Q.245, P.246, F.247, G.248, Q.249, L.272, S.273 Ligands: IOD.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.245, A:F.247, A:G.248, A:S.273 Water bridges: A:W.236

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

CL.7: 3 residues within 4Å: Chain A: I.140, S.141, M.144 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: D.89, P.90, R.94 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain A: R.15, L.18, V.62, I.64, P.104, C.106 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: Q.125, L.126, L.241 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Richter, H. et al., DNA-Encoded Library-Derived DDR1 Inhibitor Prevents Fibrosis and Renal Function Loss in a Genetic Mouse Model of Alport Syndrome. Acs Chem.Biol. (2019)

Release Date

2018-11-28

Peptides

Epithelial discoidin domain-containing receptor 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Epithelial discoidin domain-containing receptor 1

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