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7X8X

Structural insights into mycobacterium tuberculosis clpp1p2 inhibition by cediranib: implications for developing antimicrobial agents targeting clp protease

PDB DOI: 10.2210/pdb7x8x/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.)

Deposited: 2022-03-15
Deposition Author(s): Bao, R. , Luo, Y.F. , Yang, Y. , Zhou, Y.Z. , Zhu, Y.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.24 Å

7x8x
Literature

Structural insights into mycobacterium tuberculosis clpp1p2 inhibition by cediranib: implications for developing antimicrobial agents targeting clp protease

Bao, R. , Luo, Y.F. , Yang, Y. , Zhou, Y.Z. , Zhu, Y.B.

Primary Citation of Related Structures: 7X8X


Proteins
Molecule Chains Sequence Length Organism Sequence
ATP-dependent Clp protease proteolytic subunit 2 A 197 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) YILPSFIEHSSFGVKESNPYNKLFEERIIFLGVQVDDASANDIMAQLLVLESLDPDRDITMYINSPGGGFTSLMAIYDTMQYVRADIQTVCLGQAASAAAVLLAAGTPGKRMALPNARVLIHQPSLSGVIQGQFSDLEIQAAEIERMRTLMETTLARHTGKDAGVIRKDTDRDKILTAEEAKDYGIIDTVLEYRKLS
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide O 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide C 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide Q 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide F 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide S 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide H 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide T 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide J 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide V 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide L 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide X 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide E 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
ATP-dependent Clp protease proteolytic subunit 1 B 177 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) LTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGMAIYDTMVLAPCDIATYAMGMAASMGEFLLAAGTKGKRYALPHARILMHQPLGGVTGSAADIAIQAEQFAVIKKEMFRLNAEFTGQPIERIEADSDRDRWFTAAEALEYGFVDHIITR
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide P 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
ATP-dependent Clp protease proteolytic subunit 1 D 177 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) LTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGMAIYDTMVLAPCDIATYAMGMAASMGEFLLAAGTKGKRYALPHARILMHQPLGGVTGSAADIAIQAEQFAVIKKEMFRLNAEFTGQPIERIEADSDRDRWFTAAEALEYGFVDHIITR
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide R 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide I 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide U 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide K 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide W 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide M 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide Y 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide N 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide Z 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide G 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide 0 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide 1 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide 2 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide 3 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
4-[[3,5-bis(fluoranyl)phenyl]methyl]-N-[(4-bromophenyl)methyl]piperazine-1-carboxamide 4 3 Taenia Saginata , Mycobacterium Vanbaalenii Pyr-1 , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) XLL
Experimental Data

Method: X-RAY DIFFRACTION

Deposited Date: 2022-03-15
Deposition Author(s): Bao, R. , Luo, Y.F. , Yang, Y. , Zhou, Y.Z. , Zhu, Y.B.