SMTL ID : 7x8x.2 (1 other biounit)

structural insights into Mycobacterium tuberculosis ClpP1P2 inhibition by Cediranib: implications for developing antimicrobial agents targeting Clp protease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.24 Å

Oligo State

hetero-7-7-mer

Ligands

14 x BEZ- LEU- LEU: 4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide(Non-covalent)

BEZ-LEU-LEU.1: 19 residues within 4Å: Chain H: F.134 Chain I: G.53, G.54, S.55, I.56, S.57, S.83, M.84, F.87, H.108, Q.109, P.110, L.111, G.112, G.113, F.128, I.131, M.135 Ligands: AI4.17 10 PLIP interactions: 9 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: I:I.56, I:F.128 Hydrogen bonds: I:G.54, I:G.54, I:I.56, I:M.84, I:L.111, I:L.111 Salt bridges: I:H.108 pi-Stacking: H:F.134 BEZ-LEU-LEU.2: 17 residues within 4Å: Chain H: P.66, G.67, G.68, G.69, F.70, L.73, S.97, A.98, V.101, H.122, P.124, S.125, L.126, S.127, I.144, M.147, M.151 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:F.70, H:F.70, H:L.73, H:P.124, H:I.144 Hydrogen bonds: H:G.68, H:S.125, H:S.125, H:S.125 BEZ-LEU-LEU.3: 19 residues within 4Å: Chain A: F.134 Chain B: G.53, G.54, S.55, I.56, S.57, S.83, M.84, F.87, H.108, Q.109, P.110, L.111, G.112, G.113, F.128, I.131, M.135 Ligands: AI4.19 12 PLIP interactions: 1 interactions with chain A, 11 interactions with chain B pi-Stacking: A:F.134 Hydrophobic interactions: B:P.110, B:F.128, B:I.131 Hydrogen bonds: B:G.54, B:G.54, B:I.56, B:S.83, B:M.84, B:L.111, B:L.111 Salt bridges: B:H.108 BEZ-LEU-LEU.4: 15 residues within 4Å: Chain A: G.68, G.69, F.70, L.73, S.97, A.98, V.101, H.122, P.124, S.125, L.126, S.127, I.144, M.147, M.151 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.70, A:F.70 Hydrogen bonds: A:G.68, A:F.70, A:S.125, A:S.125, A:S.127 BEZ-LEU-LEU.5: 20 residues within 4Å: Chain E: F.134 Chain K: G.53, G.54, S.55, I.56, S.57, S.83, M.84, F.87, H.108, Q.109, P.110, L.111, G.112, G.113, F.128, I.131, M.135, N.139 Ligands: AI4.15 11 PLIP interactions: 10 interactions with chain K, 1 interactions with chain E Hydrophobic interactions: K:I.56, K:F.128, K:I.131, E:F.134 Hydrogen bonds: K:G.54, K:G.54, K:I.56, K:M.84, K:L.111, K:L.111 Salt bridges: K:H.108 BEZ-LEU-LEU.6: 18 residues within 4Å: Chain E: P.66, G.67, G.68, G.69, F.70, L.73, S.97, A.98, V.101, H.122, Q.123, P.124, S.125, L.126, S.127, I.144, M.147, M.151 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:F.70, E:F.70, E:L.73, E:A.98 Hydrogen bonds: E:G.68, E:S.125, E:S.125, E:S.127 BEZ-LEU-LEU.7: 19 residues within 4Å: Chain C: F.134 Chain D: G.53, G.54, S.55, I.56, S.57, S.83, M.84, F.87, H.108, Q.109, P.110, L.111, G.112, G.113, F.128, I.131, M.135 Ligands: AI4.16 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:M.84, D:F.128, D:I.131, C:F.134, C:F.134 Hydrogen bonds: D:G.54, D:G.54, D:G.54, D:I.56, D:S.83, D:M.84, D:L.111, D:L.111 Salt bridges: D:H.108 BEZ-LEU-LEU.8: 17 residues within 4Å: Chain C: Q.34, G.68, G.69, F.70, T.71, L.73, S.97, A.98, V.101, H.122, P.124, S.125, L.126, S.127, I.144, M.147, M.151 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.70, C:F.70, C:P.124 Hydrogen bonds: C:G.68, C:S.125, C:S.125 BEZ-LEU-LEU.9: 18 residues within 4Å: Chain F: F.134 Chain G: G.53, G.54, S.55, I.56, S.83, M.84, F.87, H.108, Q.109, P.110, L.111, G.112, G.113, F.128, I.131, M.135 Ligands: AI4.21 10 PLIP interactions: 9 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:I.56, G:F.128 Hydrogen bonds: G:G.54, G:G.54, G:I.56, G:S.83, G:M.84, G:L.111, G:L.111 pi-Stacking: F:F.134 BEZ-LEU-LEU.10: 17 residues within 4Å: Chain F: Q.34, G.68, G.69, F.70, T.71, L.73, S.97, A.98, V.101, H.122, P.124, S.125, L.126, S.127, I.144, M.147, M.151 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:F.70, F:F.70 Hydrogen bonds: F:G.68, F:S.125, F:S.125, F:S.127 BEZ-LEU-LEU.11: 18 residues within 4Å: Chain M: F.134 Chain N: G.53, G.54, S.55, I.56, S.57, S.83, M.84, H.108, Q.109, P.110, L.111, G.112, G.113, F.128, I.131, M.135 Ligands: AI4.20 11 PLIP interactions: 1 interactions with chain M, 10 interactions with chain N pi-Stacking: M:F.134 Hydrophobic interactions: N:I.56, N:F.128, N:I.131 Hydrogen bonds: N:G.54, N:G.54, N:I.56, N:M.84, N:L.111, N:L.111 Salt bridges: N:H.108 BEZ-LEU-LEU.12: 14 residues within 4Å: Chain M: G.68, G.69, F.70, L.73, S.97, A.98, V.101, H.122, P.124, S.125, L.126, S.127, G.128, M.151 11 PLIP interactions: 11 interactions with chain M Hydrophobic interactions: M:F.70, M:F.70, M:L.73, M:A.98, M:L.126 Hydrogen bonds: M:G.68, M:F.70, M:S.125, M:S.125, M:S.127, M:G.128 BEZ-LEU-LEU.13: 18 residues within 4Å: Chain J: F.134 Chain L: G.53, G.54, S.55, I.56, S.83, M.84, F.87, H.108, Q.109, P.110, L.111, G.112, G.113, F.128, I.131, M.135 Ligands: AI4.18 10 PLIP interactions: 1 interactions with chain J, 9 interactions with chain L pi-Stacking: J:F.134 Hydrophobic interactions: L:I.56, L:F.128, L:I.131 Hydrogen bonds: L:G.54, L:G.54, L:I.56, L:M.84, L:L.111, L:L.111 BEZ-LEU-LEU.14: 18 residues within 4Å: Chain J: V.35, G.68, G.69, F.70, L.73, S.97, A.98, V.101, H.122, Q.123, P.124, S.125, L.126, S.127, G.128, I.144, M.147, M.151 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:F.70, J:F.70, J:L.73, J:A.98, J:P.124, J:L.126 Hydrogen bonds: J:G.68, J:F.70, J:S.125, J:S.127, J:S.127

7 x AI4: 4-[1-[3-[4-[(4-fluoranyl-2-methyl-1H-indol-5-yl)oxy]-6-methoxy-quinazolin-7-yl]oxypropyl]piperidin-4-yl]benzamide(Non-covalent)(Covalent)

AI4.15: 20 residues within 4Å: Chain D: G.79, M.80, H.102, A.103, R.104, W.159 Chain E: V.129, Q.131 Chain K: S.55, I.56, S.57, M.60, G.113, Q.127, I.131, E.134, M.135, L.138 Ligands: BEZ-LEU-LEU.5, BEZ-LEU-LEU.5 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain K Hydrophobic interactions: D:R.104, K:E.134 Hydrogen bonds: D:H.102, D:R.104 pi-Stacking: D:W.159 pi-Cation interactions: D:R.104 AI4.16: 19 residues within 4Å: Chain C: V.129, Q.131 Chain D: S.55, I.56, S.57, M.60, G.113, Q.127, I.131, E.134, L.138 Chain G: G.79, M.80, H.102, A.103, R.104, W.159 Ligands: BEZ-LEU-LEU.7, BEZ-LEU-LEU.7 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain G Hydrophobic interactions: D:I.56, D:I.131, D:E.134, G:R.104, G:R.104 Hydrogen bonds: G:H.102, G:R.104 pi-Stacking: G:W.159 pi-Cation interactions: G:R.104 AI4.17: 21 residues within 4Å: Chain B: G.79, M.80, H.102, A.103, R.104, W.159 Chain H: V.129, Q.131 Chain I: S.55, I.56, S.57, M.60, G.112, G.113, T.115, Q.127, I.131, E.134, L.138 Ligands: BEZ-LEU-LEU.1, BEZ-LEU-LEU.1 9 PLIP interactions: 1 interactions with chain H, 2 interactions with chain I, 6 interactions with chain B Hydrogen bonds: H:Q.131, B:H.102, B:R.104 Hydrophobic interactions: I:I.56, I:I.131, B:R.104, B:W.159 pi-Stacking: B:W.159 pi-Cation interactions: B:R.104 AI4.18: 20 residues within 4Å: Chain I: G.79, M.80, H.102, A.103, R.104, W.159 Chain J: Q.131 Chain L: S.55, I.56, S.57, M.60, G.112, G.113, Q.127, I.131, E.134, M.135, L.138 Ligands: BEZ-LEU-LEU.13, BEZ-LEU-LEU.13 7 PLIP interactions: 3 interactions with chain L, 4 interactions with chain I Hydrophobic interactions: L:I.56, L:E.134, I:R.104 Hydrogen bonds: L:S.57, I:H.102 pi-Stacking: I:W.159 pi-Cation interactions: I:R.104 AI4.19: 21 residues within 4Å: Chain A: V.129, Q.131 Chain B: S.55, I.56, S.57, M.60, L.111, G.112, Q.127, I.131, E.134, M.135, L.138 Chain K: G.79, M.80, H.102, A.103, R.104, W.159 Ligands: BEZ-LEU-LEU.3, BEZ-LEU-LEU.3 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain K Hydrophobic interactions: B:I.131, B:E.134, K:R.104, K:R.104 Hydrogen bonds: K:H.102, K:R.104 pi-Stacking: K:W.159 pi-Cation interactions: K:R.104 AI4.20: 21 residues within 4Å: Chain L: G.79, M.80, H.102, A.103, R.104, W.159 Chain M: V.129, Q.131 Chain N: S.55, I.56, S.57, M.60, G.113, T.115, Q.127, I.131, E.134, M.135, L.138 Ligands: BEZ-LEU-LEU.11, BEZ-LEU-LEU.11 8 PLIP interactions: 7 interactions with chain L, 1 interactions with chain N Hydrophobic interactions: L:R.104, L:W.159, N:I.56 Hydrogen bonds: L:H.102, L:R.104, L:R.104 pi-Stacking: L:W.159 pi-Cation interactions: L:R.104 AI4.21: 23 residues within 4Å: Chain F: V.129, Q.131 Chain G: S.55, I.56, S.57, M.60, L.111, G.112, G.113, T.115, Q.127, I.131, E.134, M.135, L.138 Chain N: G.79, M.80, H.102, A.103, R.104, W.159 Ligands: BEZ-LEU-LEU.9, BEZ-LEU-LEU.9 9 PLIP interactions: 6 interactions with chain N, 2 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: N:R.104, N:R.104, G:I.56, G:E.134 Hydrogen bonds: N:H.102, N:R.104, F:Q.131 pi-Stacking: N:W.159 pi-Cation interactions: N:R.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Discovery and Mechanistic Study of Novel Mycobacterium tuberculosis ClpP1P2 Inhibitors. J.Med.Chem. (2023)

Release Date

2023-04-12

Peptides

ATP-dependent Clp protease proteolytic subunit 2: ACEFHJM
ATP-dependent Clp protease proteolytic subunit 1: BDGIKLN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

C
Q

E
S

F
T

H
V

J
X

M
a

B
P

D
R

G
U

I
W

K
Y

L
Z

N
b

ATP-dependent Clp protease proteolytic subunit 2

ATP-dependent Clp protease proteolytic subunit 1

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