- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.42 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x 7ZH: methyl 6-[4-[[~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]carbamimidoyl]amino]butylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate(Non-covalent)
7ZH.1: 37 residues within 4Å:- Chain A: F.12, R.15, Y.24, F.25, F.27, Y.28, Q.33, Q.34, M.37, R.43, G.67, G.69, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, P.133, M.134, G.135, Y.136, N.140, E.141, M.143, S.146, H.289, W.290, L.344, K.345, N.346, P.347, F.349
- Ligands: EDO.2
19 PLIP interactions:19 interactions with chain A- Hydrophobic interactions: A:F.27, A:Y.136, A:P.347
- Hydrogen bonds: A:Y.24, A:Y.28, A:Q.34, A:G.69, A:A.90, A:S.91, A:V.117, A:E.118, A:E.132, A:N.140, A:E.141
- Water bridges: A:N.140, A:L.344
- Salt bridges: A:E.132
- pi-Stacking: A:F.25, A:F.349
7ZH.6: 36 residues within 4Å:- Chain B: F.12, R.15, Y.24, F.25, F.27, Y.28, Q.33, Q.34, M.37, G.67, G.69, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, P.133, M.134, G.135, Y.136, N.140, E.141, M.143, S.146, H.289, W.290, L.344, K.345, N.346, P.347, F.349
- Ligands: EDO.7
18 PLIP interactions:18 interactions with chain B- Hydrophobic interactions: B:F.27, B:Y.136, B:W.290, B:P.347, B:F.349
- Hydrogen bonds: B:Y.24, B:Q.34, B:G.69, B:A.90, B:S.91, B:V.117, B:E.118, B:N.140, B:E.141, B:E.141
- Salt bridges: B:E.132, B:E.141
- pi-Stacking: B:F.25
7ZH.9: 35 residues within 4Å:- Chain C: F.12, R.15, Y.24, F.25, F.27, Y.28, Q.33, Q.34, M.37, G.67, G.69, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, P.133, M.134, Y.136, N.140, E.141, M.143, S.146, H.289, W.290, L.344, K.345, N.346, P.347, F.349
- Ligands: EDO.10
16 PLIP interactions:16 interactions with chain C- Hydrophobic interactions: C:F.27, C:Y.136, C:W.290, C:P.347
- Hydrogen bonds: C:Y.24, C:Y.28, C:Y.28, C:Q.34, C:A.90, C:S.91, C:V.117, C:E.118, C:N.140
- Salt bridges: C:E.132
- pi-Stacking: C:F.25, C:F.349
7ZH.14: 35 residues within 4Å:- Chain D: F.12, R.15, Y.24, F.25, F.27, Y.28, Q.33, Q.34, M.37, G.67, G.69, V.88, E.89, A.90, S.91, G.115, K.116, V.117, E.118, E.132, P.133, M.134, G.135, Y.136, N.140, E.141, M.143, S.146, H.289, W.290, L.344, K.345, P.347, F.349
- Ligands: EDO.15
19 PLIP interactions:19 interactions with chain D- Hydrophobic interactions: D:F.27, D:Y.136, D:P.347, D:F.349, D:F.349
- Hydrogen bonds: D:Y.24, D:G.69, D:A.90, D:S.91, D:V.117, D:E.118, D:P.133, D:M.134, D:N.140, D:E.141, D:E.141
- Salt bridges: D:E.132, D:E.141
- pi-Stacking: D:F.25
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.2: 6 residues within 4Å:- Chain A: Y.24, F.27, Y.28, E.141, K.345
- Ligands: 7ZH.1
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.141
EDO.3: 6 residues within 4Å:- Chain A: D.40, L.287, T.288, H.289, Y.291, Y.351
No protein-ligand interaction detected (PLIP)EDO.4: 3 residues within 4Å:- Chain A: D.267, W.278, S.280
No protein-ligand interaction detected (PLIP)EDO.5: 6 residues within 4Å:- Chain A: Q.39
- Chain B: F.187, Q.190, F.193
- Chain D: L.258, F.302
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:Q.39, B:Q.190
EDO.7: 5 residues within 4Å:- Chain B: Y.24, F.27, Y.28, E.141
- Ligands: 7ZH.6
No protein-ligand interaction detected (PLIP)EDO.8: 3 residues within 4Å:- Chain B: D.267, W.278, S.280
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:D.267
EDO.10: 6 residues within 4Å:- Chain C: Q.23, Y.24, F.27, Y.28, E.141
- Ligands: 7ZH.9
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:Q.23, C:E.141
EDO.11: 5 residues within 4Å:- Chain C: K.151, L.154, K.155, P.156, G.158
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:K.151, C:P.156
EDO.12: 2 residues within 4Å:- Chain C: W.278, S.280
No protein-ligand interaction detected (PLIP)EDO.13: 5 residues within 4Å:- Chain C: D.40, L.287, T.288, H.289, Y.291
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:Y.291
EDO.15: 4 residues within 4Å:- Chain D: Y.24, F.27, E.141
- Ligands: 7ZH.14
No protein-ligand interaction detected (PLIP)EDO.16: 3 residues within 4Å:- Chain D: D.267, W.278, S.280
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Iannelli, G. et al., Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction-Reconstruction and Fragment-Growing Approach. J.Med.Chem. (2022)
- Release Date
- 2022-04-06
- Peptides
- Histone-arginine methyltransferase CARM1: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.42 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x 7ZH: methyl 6-[4-[[~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]carbamimidoyl]amino]butylcarbamoylamino]-4-oxidanyl-naphthalene-2-carboxylate(Non-covalent)
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Iannelli, G. et al., Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction-Reconstruction and Fragment-Growing Approach. J.Med.Chem. (2022)
- Release Date
- 2022-04-06
- Peptides
- Histone-arginine methyltransferase CARM1: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D