- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-octamer
- Ligands
- 8 x CRN: N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE(Non-covalent)
- 8 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)(Covalent)
ADP.2: 19 residues within 4Å:- Chain A: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358
- Ligands: PO4.3, MG.4
16 PLIP interactions:16 interactions with chain A- Hydrogen bonds: A:S.151, A:S.151, A:R.315, A:H.319, A:H.319, A:G.347, A:V.348
- Salt bridges: A:R.153, A:R.153, A:R.155, A:R.259, A:R.315, A:R.315, A:R.343, A:R.343
- pi-Stacking: A:H.319
ADP.6: 20 residues within 4Å:- Chain B: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, T.345, G.346, G.347, V.348, D.358
- Ligands: PO4.7, MG.8
16 PLIP interactions:16 interactions with chain B- Hydrogen bonds: B:R.153, B:R.315, B:G.317, B:H.319, B:T.345, B:G.346, B:V.348
- Salt bridges: B:R.153, B:R.153, B:R.155, B:R.259, B:R.315, B:R.315, B:R.343, B:R.343
- pi-Stacking: B:H.319
ADP.9: 19 residues within 4Å:- Chain C: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358
- Ligands: PO4.10, MG.12
16 PLIP interactions:16 interactions with chain C- Hydrogen bonds: C:S.151, C:R.153, C:R.315, C:G.317, C:H.319, C:G.347, C:V.348
- Salt bridges: C:R.153, C:R.153, C:R.155, C:R.259, C:R.315, C:R.315, C:R.343, C:R.343
- pi-Stacking: C:H.319
ADP.14: 19 residues within 4Å:- Chain D: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358
- Ligands: PO4.15, MG.16
16 PLIP interactions:16 interactions with chain D- Hydrogen bonds: D:S.151, D:S.151, D:R.315, D:H.319, D:H.319, D:G.347, D:V.348
- Salt bridges: D:R.153, D:R.153, D:R.155, D:R.259, D:R.315, D:R.315, D:R.343, D:R.343
- pi-Stacking: D:H.319
ADP.18: 21 residues within 4Å:- Chain E: S.151, S.152, R.153, R.155, H.214, L.216, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, T.345, G.346, G.347, V.348, D.358
- Ligands: PO4.19, MG.20
17 PLIP interactions:17 interactions with chain E- Hydrogen bonds: E:R.153, E:R.315, E:G.317, E:H.319, E:H.319, E:G.346, E:G.346, E:V.348
- Salt bridges: E:R.153, E:R.153, E:R.155, E:R.259, E:R.315, E:R.315, E:R.343, E:R.343
- pi-Stacking: E:H.319
ADP.22: 19 residues within 4Å:- Chain F: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358
- Ligands: PO4.23, MG.24
16 PLIP interactions:16 interactions with chain F- Hydrogen bonds: F:S.151, F:S.151, F:R.315, F:H.319, F:H.319, F:G.347, F:V.348
- Salt bridges: F:R.153, F:R.153, F:R.155, F:R.259, F:R.315, F:R.315, F:R.343, F:R.343
- pi-Stacking: F:H.319
ADP.26: 19 residues within 4Å:- Chain G: S.151, S.152, R.153, R.155, H.214, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358
- Ligands: PO4.27, MG.28
17 PLIP interactions:17 interactions with chain G- Hydrogen bonds: G:S.151, G:S.151, G:R.153, G:R.315, G:H.319, G:H.319, G:G.347, G:V.348
- Salt bridges: G:R.153, G:R.153, G:R.155, G:R.259, G:R.315, G:R.315, G:R.343, G:R.343
- pi-Stacking: G:H.319
ADP.30: 20 residues within 4Å:- Chain H: S.151, S.152, R.153, R.155, H.214, L.216, W.251, R.259, M.263, R.315, G.317, V.318, H.319, R.343, G.346, G.347, V.348, D.358
- Ligands: PO4.31, MG.32
14 PLIP interactions:14 interactions with chain H- Hydrogen bonds: H:S.151, H:S.151, H:R.315, H:H.319, H:V.348
- Salt bridges: H:R.153, H:R.153, H:R.155, H:R.259, H:R.315, H:R.315, H:R.343, H:R.343
- pi-Stacking: H:H.319
- 8 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.3: 9 residues within 4Å:- Chain A: R.155, Q.255, R.259, N.309, R.343, V.348
- Ligands: CRN.1, ADP.2, MG.4
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:Q.255, A:N.309, A:N.309
- Salt bridges: A:R.155, A:R.259, A:R.343
PO4.7: 11 residues within 4Å:- Chain B: R.155, Q.255, R.259, N.309, R.315, R.343, V.348, R.364
- Ligands: CRN.5, ADP.6, MG.8
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:Q.255, B:N.309
- Salt bridges: B:R.155, B:R.259, B:R.343
PO4.10: 9 residues within 4Å:- Chain C: R.155, Q.255, R.259, N.309, R.343, V.348
- Ligands: ADP.9, CRN.11, MG.12
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:Q.255, C:N.309
- Salt bridges: C:R.155, C:R.259, C:R.343
PO4.15: 10 residues within 4Å:- Chain D: R.155, Q.255, R.259, N.309, R.343, V.348, R.364
- Ligands: CRN.13, ADP.14, MG.16
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:Q.255, D:N.309, D:N.309
- Salt bridges: D:R.155, D:R.259, D:R.343
PO4.19: 8 residues within 4Å:- Chain E: R.155, Q.255, R.259, N.309, R.343
- Ligands: CRN.17, ADP.18, MG.20
6 PLIP interactions:6 interactions with chain E- Hydrogen bonds: E:Q.255, E:N.309, E:N.309
- Salt bridges: E:R.155, E:R.259, E:R.343
PO4.23: 10 residues within 4Å:- Chain F: R.155, Q.255, R.259, N.309, R.315, R.343, R.364
- Ligands: CRN.21, ADP.22, MG.24
5 PLIP interactions:5 interactions with chain F- Hydrogen bonds: F:Q.255, F:N.309
- Salt bridges: F:R.155, F:R.259, F:R.343
PO4.27: 10 residues within 4Å:- Chain G: R.155, Q.255, R.259, N.309, R.343, V.348, R.364
- Ligands: CRN.25, ADP.26, MG.28
5 PLIP interactions:5 interactions with chain G- Hydrogen bonds: G:Q.255, G:N.309
- Salt bridges: G:R.155, G:R.259, G:R.343
PO4.31: 11 residues within 4Å:- Chain H: R.155, Q.255, R.259, N.309, R.315, R.343, V.348, R.364
- Ligands: CRN.29, ADP.30, MG.32
5 PLIP interactions:5 interactions with chain H- Hydrogen bonds: H:Q.255, H:N.309
- Salt bridges: H:R.155, H:R.259, H:R.343
- 8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.4: 4 residues within 4Å:- Chain A: R.259, R.343
- Ligands: ADP.2, PO4.3
No protein-ligand interaction detected (PLIP)MG.8: 4 residues within 4Å:- Chain B: Q.255, R.259
- Ligands: ADP.6, PO4.7
No protein-ligand interaction detected (PLIP)MG.12: 5 residues within 4Å:- Chain C: Q.255, R.259, R.343
- Ligands: ADP.9, PO4.10
No protein-ligand interaction detected (PLIP)MG.16: 4 residues within 4Å:- Chain D: Q.255, R.259
- Ligands: ADP.14, PO4.15
No protein-ligand interaction detected (PLIP)MG.20: 5 residues within 4Å:- Chain E: Q.255, R.259, R.343
- Ligands: ADP.18, PO4.19
No protein-ligand interaction detected (PLIP)MG.24: 4 residues within 4Å:- Chain F: R.259, R.343
- Ligands: ADP.22, PO4.23
No protein-ligand interaction detected (PLIP)MG.28: 4 residues within 4Å:- Chain G: R.259, R.343
- Ligands: ADP.26, PO4.27
No protein-ligand interaction detected (PLIP)MG.32: 4 residues within 4Å:- Chain H: Q.255, R.259
- Ligands: ADP.30, PO4.31
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Demir, M. et al., Structural basis for substrate binding, catalysis and inhibition of cancer target mitochondrial creatine kinase by a covalent inhibitor. Structure (2025)
- Release Date
- 2025-02-12
- Peptides
- Creatine kinase U-type, mitochondrial: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
H
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-octamer
- Ligands
- 8 x CRN: N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE(Non-covalent)
- 8 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)(Covalent)
- 8 x PO4: PHOSPHATE ION(Non-functional Binders)
- 8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Demir, M. et al., Structural basis for substrate binding, catalysis and inhibition of cancer target mitochondrial creatine kinase by a covalent inhibitor. Structure (2025)
- Release Date
- 2025-02-12
- Peptides
- Creatine kinase U-type, mitochondrial: ABCDEFGH
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GH
H