SMTL ID : 3q4u.2 (2 other biounits)

Crystal structure of the ACVR1 kinase domain in complex with LDN-193189

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x LDN: 4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline(Non-covalent)

LDN.1: 18 residues within 4Å: Chain A: V.16, V.24, A.35, K.37, L.65, T.85, H.86, Y.87, H.88, E.89, M.90, G.91, D.95, L.99, K.142, N.143, L.145, A.155 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.16, A:L.65, A:L.145, A:A.155 Hydrogen bonds: A:H.88, A:M.90 Water bridges: A:D.156 LDN.8: 17 residues within 4Å: Chain B: V.16, V.24, A.35, K.37, L.65, T.85, H.86, Y.87, H.88, E.89, G.91, D.95, K.142, N.143, L.145, A.155, D.156 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.16, B:V.16, B:L.65, B:L.145, B:A.155, B:D.156 Hydrogen bonds: B:H.88 Water bridges: B:M.90, B:D.95, B:D.156

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

EDO.2: 4 residues within 4Å: Chain A: K.45, F.48, R.49, E.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.45, A:R.49, A:R.49 EDO.3: 6 residues within 4Å: Chain A: P.132, M.162, H.163, S.164, Q.169, D.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.164, A:Q.169, A:D.171 EDO.4: 4 residues within 4Å: Chain A: D.71, T.73, Q.80, W.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.71 EDO.9: 4 residues within 4Å: Chain B: T.101, L.102, D.103, V.221 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.101, B:T.101 Water bridges: B:T.104 EDO.10: 7 residues within 4Å: Chain B: F.233, D.235, V.236, Q.255, R.256, P.257, N.258 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.255 Water bridges: B:F.233, B:D.235, B:N.258 EDO.11: 3 residues within 4Å: Chain B: R.182, D.240, P.241 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.182, B:R.182 EDO.12: 3 residues within 4Å: Chain B: W.29, Q.30, E.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.29

6 x FLC: CITRATE ANION(Non-covalent)

FLC.5: 7 residues within 4Å: Chain A: H.86, Y.87, H.88, E.89, K.147, K.148 Ligands: FLC.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.89, A:E.89, A:E.89, A:K.148 Water bridges: A:K.147 Salt bridges: A:H.86, A:H.86, A:H.88, A:H.88 FLC.6: 7 residues within 4Å: Chain A: K.140, K.142, T.180, R.182, N.239, D.240, P.241 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.180 Hydrogen bonds: A:D.240 Water bridges: A:R.182 Salt bridges: A:K.140, A:K.142, A:K.142, A:R.182 FLC.7: 11 residues within 4Å: Chain A: R.60, H.61, E.62, I.64, L.65, G.66, H.86, H.88, K.147, C.153 Ligands: FLC.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:H.61, A:H.61, A:E.62, A:G.66 Water bridges: A:F.67, A:F.67, A:K.147 Salt bridges: A:H.86, A:H.88, A:K.147, A:K.147 FLC.13: 7 residues within 4Å: Chain B: H.86, Y.87, H.88, E.89, K.147, K.148 Ligands: FLC.14 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:K.148 Hydrogen bonds: B:H.86, B:H.88, B:E.89, B:K.148 Water bridges: B:M.90 Salt bridges: B:H.86, B:H.88, B:H.88, B:K.147 FLC.14: 10 residues within 4Å: Chain B: H.61, E.62, I.64, L.65, G.66, H.86, H.88, K.147, C.153 Ligands: FLC.13 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:H.61, B:G.66, B:K.147 Water bridges: B:H.61, B:H.61, B:E.62 Salt bridges: B:H.86, B:H.86, B:H.88, B:K.147, B:K.147 FLC.15: 5 residues within 4Å: Chain B: I.123, K.202, T.289, A.290, L.291 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.291 Hydrogen bonds: B:K.202, B:T.289, B:T.289, B:L.291 Water bridges: B:K.202, B:K.202, B:K.202, B:K.202, B:K.202, B:A.290, B:A.290 Salt bridges: B:K.202, B:K.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanvitale, C.E. et al., A new class of small molecule inhibitor of BMP signaling. Plos One (2013)

Release Date

2011-02-09

Peptides

Activin receptor type-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Activin receptor type-1

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