- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.65 Å
- Oligo State
- hetero-14-14-mer
- Ligands
- 20 x DMF: DIMETHYLFORMAMIDE(Non-covalent)
- 14 x M6Y: N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-1,4-dioxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide (non-preferred name)(Non-covalent)
M6Y.9: 23 residues within 4Å:- Chain H: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, R.32, K.33, I.45, G.47, T.48, A.49, A.52, V.53
- Chain I: S.122, D.124, A.125, A.126, G.128, W.129, N.130
- Ligands: CIT.10
20 PLIP interactions:15 interactions with chain H, 5 interactions with chain I- Hydrophobic interactions: H:V.31, H:V.31, H:K.33, H:K.33, H:A.49, H:A.52, I:N.130
- Hydrogen bonds: H:T.1, H:T.21, H:T.21, H:Q.22, H:S.27, H:G.47, H:A.49, I:D.124, I:D.124, I:A.125, I:A.126
- Water bridges: H:A.50
- Halogen bonds: H:S.20
M6Y.11: 24 residues within 4Å:- Chain I: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, V.53, L.98
- Chain J: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Ligands: CIT.12
17 PLIP interactions:12 interactions with chain I, 5 interactions with chain J- Hydrophobic interactions: I:V.31, I:V.31, I:K.33, I:A.49, I:A.52, I:L.98, J:A.126, J:N.130
- Hydrogen bonds: I:T.1, I:T.21, I:T.21, I:S.27, I:G.47, I:A.49, J:D.124, J:D.124, J:A.125
M6Y.14: 23 residues within 4Å:- Chain J: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, V.53
- Chain K: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Ligands: CIT.15
18 PLIP interactions:13 interactions with chain J, 5 interactions with chain K- Hydrophobic interactions: J:V.31, J:V.31, J:K.33, J:K.33, J:A.49, J:A.52, K:A.126, K:N.130
- Hydrogen bonds: J:T.21, J:T.21, J:S.27, J:G.47, J:A.49, K:D.124, K:D.124, K:A.125
- Water bridges: J:Q.22, J:A.50
M6Y.18: 23 residues within 4Å:- Chain K: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, V.53
- Chain L: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Ligands: CIT.19
18 PLIP interactions:4 interactions with chain L, 14 interactions with chain K- Hydrophobic interactions: L:N.130, K:V.31, K:V.31, K:K.33, K:K.33, K:A.49, K:A.52
- Hydrogen bonds: L:D.124, L:D.124, L:A.125, K:T.1, K:T.21, K:T.21, K:Q.22, K:S.27, K:G.47, K:A.49
- Water bridges: K:A.50
M6Y.20: 24 residues within 4Å:- Chain L: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, R.32, K.33, I.45, G.47, T.48, A.49, A.52, V.53
- Chain M: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Ligands: CIT.21
18 PLIP interactions:13 interactions with chain L, 5 interactions with chain M- Hydrophobic interactions: L:V.31, L:K.33, L:K.33, L:A.49, L:A.52, M:A.126, M:N.130
- Hydrogen bonds: L:T.1, L:T.21, L:T.21, L:S.27, L:G.47, L:A.49, M:D.124, M:D.124, M:A.125
- Water bridges: L:Q.22
- Halogen bonds: L:S.20
M6Y.22: 25 residues within 4Å:- Chain M: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, R.32, K.33, I.45, G.47, T.48, A.49, A.52, V.53, L.98
- Chain N: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Ligands: CIT.23
18 PLIP interactions:13 interactions with chain M, 5 interactions with chain N- Hydrophobic interactions: M:V.31, M:K.33, M:K.33, M:A.49, M:A.52, M:L.98, N:N.130
- Hydrogen bonds: M:T.1, M:T.21, M:T.21, M:S.27, M:G.47, M:A.49, N:D.124, N:D.124, N:A.125, N:A.126
- Water bridges: M:A.50
M6Y.24: 24 residues within 4Å:- Chain H: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Chain N: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, R.32, K.33, I.45, G.47, T.48, A.49, A.52, V.53
- Ligands: CIT.25
15 PLIP interactions:12 interactions with chain N, 3 interactions with chain H- Hydrophobic interactions: N:V.31, N:V.31, N:K.33, N:K.33, N:A.49, N:A.52, H:N.130
- Hydrogen bonds: N:T.21, N:T.21, N:Q.22, N:S.27, N:G.47, N:A.49, H:D.124, H:A.125
M6Y.35: 24 residues within 4Å:- Chain V: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, R.32, K.33, I.45, G.47, T.48, A.49, A.52, V.53
- Chain W: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Ligands: CIT.36
15 PLIP interactions:12 interactions with chain V, 3 interactions with chain W- Hydrophobic interactions: V:V.31, V:V.31, V:K.33, V:K.33, V:A.49, V:A.52, W:N.130
- Hydrogen bonds: V:T.21, V:T.21, V:S.27, V:G.47, V:A.49, W:D.124, W:A.125
- Water bridges: V:A.50
M6Y.37: 24 residues within 4Å:- Chain W: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, R.32, K.33, I.45, G.47, T.48, A.49, A.52, V.53
- Chain X: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Ligands: CIT.38
19 PLIP interactions:4 interactions with chain X, 15 interactions with chain W- Hydrophobic interactions: X:N.130, W:V.31, W:V.31, W:K.33, W:K.33, W:A.49, W:A.52
- Hydrogen bonds: X:D.124, X:A.125, X:A.126, W:T.1, W:T.21, W:T.21, W:S.27, W:G.47, W:A.49
- Water bridges: W:Q.22, W:Q.22, W:Q.22
M6Y.39: 24 residues within 4Å:- Chain X: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, V.53, L.98
- Chain Y: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Ligands: CIT.40
18 PLIP interactions:5 interactions with chain Y, 13 interactions with chain X- Hydrophobic interactions: Y:A.126, Y:N.130, X:V.31, X:K.33, X:K.33, X:A.49, X:A.52, X:L.98
- Hydrogen bonds: Y:D.124, Y:D.124, X:T.1, X:T.21, X:T.21, X:S.27, X:G.47, X:A.49
- Water bridges: Y:A.125, X:A.50
M6Y.41: 23 residues within 4Å:- Chain Y: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, V.53
- Chain Z: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Ligands: CIT.42
16 PLIP interactions:12 interactions with chain Y, 4 interactions with chain Z- Hydrophobic interactions: Y:V.31, Y:K.33, Y:K.33, Y:A.49, Y:A.52, Z:A.126, Z:N.130
- Hydrogen bonds: Y:T.21, Y:T.21, Y:Q.22, Y:S.27, Y:G.47, Y:A.49, Z:D.124
- Water bridges: Y:A.50, Z:A.125
M6Y.43: 23 residues within 4Å:- Chain 0: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Chain Z: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, V.53
- Ligands: CIT.44
14 PLIP interactions:3 interactions with chain 0, 11 interactions with chain Z- Hydrophobic interactions: 0:N.130, Z:K.33, Z:K.33, Z:A.49, Z:A.52
- Hydrogen bonds: 0:D.124, 0:A.125, Z:T.21, Z:T.21, Z:Q.22, Z:S.27, Z:G.47, Z:A.49
- Water bridges: Z:A.50
M6Y.45: 24 residues within 4Å:- Chain 0: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, K.33, I.45, G.47, T.48, A.49, A.52, V.53, L.98
- Chain 1: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Ligands: CIT.46
17 PLIP interactions:12 interactions with chain 0, 5 interactions with chain 1- Hydrophobic interactions: 0:V.31, 0:V.31, 0:K.33, 0:K.33, 0:A.49, 0:A.52, 0:L.98, 1:A.126, 1:N.130
- Hydrogen bonds: 0:T.21, 0:T.21, 0:S.27, 0:G.47, 0:A.49, 1:D.124, 1:A.125, 1:A.126
M6Y.47: 24 residues within 4Å:- Chain 1: T.1, R.19, S.20, T.21, Q.22, S.27, V.31, R.32, K.33, I.45, G.47, T.48, A.49, A.52, V.53
- Chain V: S.122, F.123, D.124, A.125, A.126, G.128, W.129, N.130
- Ligands: CIT.48
18 PLIP interactions:13 interactions with chain 1, 5 interactions with chain V- Hydrophobic interactions: 1:V.31, 1:V.31, 1:K.33, 1:K.33, 1:A.49, 1:A.52, V:A.126, V:N.130
- Hydrogen bonds: 1:T.1, 1:T.21, 1:T.21, 1:Q.22, 1:S.27, 1:G.47, 1:A.49, V:D.124, V:A.125, V:A.126
- 14 x CIT: CITRIC ACID(Non-functional Binders)
CIT.10: 9 residues within 4Å:- Chain H: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Chain Y: N.24
- Ligands: M6Y.9
9 PLIP interactions:8 interactions with chain H, 1 interactions with chain Y- Hydrogen bonds: H:T.1, H:T.1, H:T.1, H:G.47, H:S.141, Y:N.24
- Water bridges: H:T.21, H:T.21
- Salt bridges: H:K.33
CIT.12: 9 residues within 4Å:- Chain I: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Chain X: N.24
- Ligands: M6Y.11
7 PLIP interactions:6 interactions with chain I, 1 interactions with chain X- Hydrogen bonds: I:T.1, I:T.1, I:T.1, I:G.47, I:S.141, X:N.24
- Salt bridges: I:K.33
CIT.15: 9 residues within 4Å:- Chain J: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Chain W: N.24
- Ligands: M6Y.14
8 PLIP interactions:1 interactions with chain W, 7 interactions with chain J- Hydrogen bonds: W:N.24, J:T.1, J:T.1, J:T.1, J:G.47, J:S.141
- Hydrophobic interactions: J:A.180
- Salt bridges: J:K.33
CIT.19: 9 residues within 4Å:- Chain K: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Chain V: N.24
- Ligands: M6Y.18
6 PLIP interactions:1 interactions with chain V, 5 interactions with chain K- Hydrogen bonds: V:N.24, K:T.1, K:T.1, K:G.47, K:S.141
- Salt bridges: K:K.33
CIT.21: 9 residues within 4Å:- Chain 1: N.24
- Chain L: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Ligands: M6Y.20
6 PLIP interactions:5 interactions with chain L, 1 interactions with chain 1- Hydrogen bonds: L:T.1, L:T.1, L:G.47, L:S.141, 1:N.24
- Salt bridges: L:K.33
CIT.23: 8 residues within 4Å:- Chain 0: N.24
- Chain M: T.1, A.46, G.47, G.140, S.141, A.180
- Ligands: M6Y.22
6 PLIP interactions:5 interactions with chain M, 1 interactions with chain 0- Hydrogen bonds: M:T.1, M:G.47, M:S.141, M:S.141, 0:N.24
- Salt bridges: M:K.33
CIT.25: 9 residues within 4Å:- Chain N: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Chain Z: N.24
- Ligands: M6Y.24
6 PLIP interactions:5 interactions with chain N, 1 interactions with chain Z- Hydrogen bonds: N:T.1, N:T.21, N:G.47, N:S.141, Z:N.24
- Salt bridges: N:K.33
CIT.36: 9 residues within 4Å:- Chain K: N.24
- Chain V: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Ligands: M6Y.35
11 PLIP interactions:1 interactions with chain K, 10 interactions with chain V- Hydrogen bonds: K:N.24, V:T.1, V:T.1, V:T.1, V:T.21, V:T.21, V:G.47, V:S.141
- Water bridges: V:T.21, V:T.21
- Salt bridges: V:K.33
CIT.38: 9 residues within 4Å:- Chain J: N.24
- Chain W: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Ligands: M6Y.37
11 PLIP interactions:10 interactions with chain W, 1 interactions with chain J- Hydrogen bonds: W:T.1, W:T.1, W:T.1, W:T.21, W:G.47, W:G.47, W:S.141, J:N.24
- Water bridges: W:T.1, W:T.1
- Salt bridges: W:K.33
CIT.40: 9 residues within 4Å:- Chain I: N.24
- Chain X: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Ligands: M6Y.39
9 PLIP interactions:1 interactions with chain I, 8 interactions with chain X- Hydrogen bonds: I:N.24, X:T.1, X:T.1, X:T.1, X:G.47, X:G.47, X:S.141
- Water bridges: X:T.21
- Salt bridges: X:K.33
CIT.42: 9 residues within 4Å:- Chain H: N.24
- Chain Y: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Ligands: M6Y.41
8 PLIP interactions:7 interactions with chain Y, 1 interactions with chain H- Hydrogen bonds: Y:T.1, Y:T.1, Y:G.47, Y:G.47, Y:S.141, H:N.24
- Water bridges: Y:T.21
- Salt bridges: Y:K.33
CIT.44: 8 residues within 4Å:- Chain N: N.24
- Chain Z: T.1, T.21, G.47, G.140, S.141, A.180
- Ligands: M6Y.43
8 PLIP interactions:7 interactions with chain Z, 1 interactions with chain N- Hydrogen bonds: Z:T.1, Z:T.1, Z:T.21, Z:G.47, Z:G.47, Z:S.141, N:N.24
- Salt bridges: Z:K.33
CIT.46: 9 residues within 4Å:- Chain 0: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Chain M: N.24
- Ligands: M6Y.45
9 PLIP interactions:8 interactions with chain 0, 1 interactions with chain M- Hydrogen bonds: 0:T.1, 0:T.1, 0:T.21, 0:G.47, 0:S.141, M:N.24
- Water bridges: 0:T.21, 0:T.21
- Salt bridges: 0:K.33
CIT.48: 9 residues within 4Å:- Chain 1: T.1, T.21, A.46, G.47, G.140, S.141, A.180
- Chain L: N.24
- Ligands: M6Y.47
11 PLIP interactions:10 interactions with chain 1, 1 interactions with chain L- Hydrogen bonds: 1:T.1, 1:T.1, 1:T.1, 1:T.21, 1:G.47, 1:G.47, 1:S.141, L:N.24
- Water bridges: 1:T.1, 1:T.21
- Salt bridges: 1:K.33
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhan, W. et al., Selective Phenylimidazole-Based Inhibitors of theMycobacterium tuberculosisProteasome. J.Med.Chem. (2019)
- Release Date
- 2019-10-09
- Peptides
- Proteasome subunit alpha: ABCDEFGOPQRSTU
Proteasome subunit beta: HIJKLMNVWXYZ01 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GO
OP
PQ
QR
RS
ST
TU
UH
HI
IJ
JK
KL
LM
MN
NV
VW
WX
XY
YZ
Z0
a1
b
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.65 Å
- Oligo State
- hetero-14-14-mer
- Ligands
- 20 x DMF: DIMETHYLFORMAMIDE(Non-covalent)
- 14 x M6Y: N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-1,4-dioxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide (non-preferred name)(Non-covalent)
- 14 x CIT: CITRIC ACID(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhan, W. et al., Selective Phenylimidazole-Based Inhibitors of theMycobacterium tuberculosisProteasome. J.Med.Chem. (2019)
- Release Date
- 2019-10-09
- Peptides
- Proteasome subunit alpha: ABCDEFGOPQRSTU
Proteasome subunit beta: HIJKLMNVWXYZ01 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
FG
GO
OP
PQ
QR
RS
ST
TU
UH
HI
IJ
JK
KL
LM
MN
NV
VW
WX
XY
YZ
Z0
a1
b