SMTL ID : 3q4u.1 (2 other biounits)

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

Coordinates

PDB Format

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: 16 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, G.91, D.95, K.142, N.143, L.145, A.155 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.16, A:V.24, A:L.65, A:L.145, A:A.155 Hydrogen bonds: A:H.88 Water bridges: A:D.156 LDN.9: 15 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, K.142, N.143, L.145, A.155 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.16, B:V.24, B:L.65, B:L.145, B:A.155 Hydrogen bonds: B:H.88 Water bridges: B:D.156

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

EDO.2: 5 residues within 4Å: Chain A: D.9, T.11, S.28, W.29, Q.30 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.11, A:T.11, A:Q.30 Water bridges: A:G.31 EDO.3: 4 residues within 4Å: Chain A: T.73, R.75, S.78, Q.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.78, A:Q.80 Water bridges: A:R.75 EDO.4: 6 residues within 4Å: Chain A: Y.96, T.101, L.102, D.103, S.106 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.96, A:D.103, A:D.103, A:S.106 EDO.5: 3 residues within 4Å: Chain A: T.100, T.101 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.101 EDO.6: 3 residues within 4Å: Chain A: R.182, D.240, P.241 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.182, A:R.182, A:D.240 EDO.10: 8 residues within 4Å: Chain B: H.61, I.64, L.65, G.66, H.86, H.88, K.147, C.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.66, B:H.88 EDO.11: 6 residues within 4Å: Chain B: Y.96, T.100, T.101, L.102, D.103, S.106 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.103, B:D.103, B:S.106

6 x FLC: CITRATE ANION(Non-covalent)

FLC.7: 7 residues within 4Å: Chain A: H.86, Y.87, H.88, E.89, K.147, K.148 Ligands: FLC.8 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.87, A:H.88, A:E.89, A:K.148 Water bridges: A:M.90, A:N.149 Salt bridges: A:H.86, A:H.88, A:H.88, A:K.147 FLC.8: 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.7 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:H.61, A:G.66, A:K.147 Water bridges: A:E.62, A:K.147 Salt bridges: A:H.86, A:H.86, A:H.88, A:K.147, A:K.147 FLC.12: 5 residues within 4Å: Chain B: Y.87, H.88, E.89, K.147, K.148 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.87, B:H.88, B:E.89, B:K.148 Water bridges: B:Y.87, B:M.90, B:N.149 Salt bridges: B:H.88, B:H.88, B:K.147 FLC.13: 4 residues within 4Å: Chain B: H.120, I.123, L.291, K.294 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.123 Hydrogen bonds: B:K.294, B:K.294 Water bridges: B:H.61, B:H.120 Salt bridges: B:H.120, B:K.294 FLC.14: 6 residues within 4Å: Chain B: H.122, I.123, K.202, T.289, A.290, L.291 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.123 Hydrogen bonds: B:T.289, B:A.290, B:L.291 Water bridges: B:H.122, B:K.202 Salt bridges: B:H.122, B:K.202, B:K.202 FLC.15: 7 residues within 4Å: Chain B: K.140, K.142, T.180, R.182, N.239, D.240, P.241 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:T.180 Hydrogen bonds: B:D.240, B:D.240 Water bridges: B:K.140, B:K.140 Salt bridges: B:K.140, B:K.142, B:K.142, B:R.182

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
A

B
B

Activin receptor type-1

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