3G7E

Crystal structure of E. coli Gyrase B co-complexed with PROP-2-YN-1-YL {[5-(4-PIPERIDIN-1-YL-2-PYRIDIN-3-YL-1,3-THIAZOL-5-YL)-1H-PYRAZOL-3-YL]METHYL}CARBAMATE inhibitor

PDB DOI: https://doi.org/10.2210/pdb3G7E/pdb

Classification: Isomerase/Isomerase inhibitor
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-09 Released: 2010-02-09
Deposition Author(s): Wei, Y., Charifson, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.234
R-Value Work: 0.206
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Discovery of pyrazolthiazoles as novel and potent inhibitors of bacterial gyrase.

Ronkin, S.M., Badia, M., Bellon, S., Grillot, A.L., Gross, C.H., Grossman, T.H., Mani, N., Parsons, J.D., Stamos, D., Trudeau, M., Wei, Y., Charifson, P.S.

(2010) Bioorg Med Chem Lett 20: 2828-2831

PubMed: 20356737 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2010.03.052
Primary Citation of Related Structures:
3G75, 3G7B, 3G7E

PubMed Abstract:
Bacterial DNA gyrase is an attractive target for the investigation of new antibacterial agents. Inhibitors of the GyrB subunit, which contains the ATP-binding site, are described in this communication. Novel, substituted 5-(1H-pyrazol-3-yl)thiazole compounds were identified as inhibitors of bacterial gyrase. Structure-guided optimization led to greater enzymatic potency and moderate antibacterial potency. Data are presented for the demonstration of selective enzyme inhibition of Escherichia coli GyrB over Staphylococcus aureus GyrB.

Organizational Affiliation

Vertex Pharmaceuticals Inc., 130 Waverly Street, Cambridge, MA 02139, USA. steven_Ronkin@vrtx.com

Macromolecule Content

Total Structure Weight: 22.72 kDa
Atom Count: 1,679
Modelled Residue Count: 203
Deposited Residue Count: 203
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A	203	Escherichia coli	Mutation(s): 0 Gene Names: ECs4634, gyrB, gyrB_1, A6592_18480, A9X72_00020, AAG43_003063, ACN68_13005, ACN81_06740, ACU57_14935, AM464_11760... ECs4634, gyrB, gyrB_1, A6592_18480, A9X72_00020, AAG43_003063, ACN68_13005, ACN81_06740, ACU57_14935, AM464_11760, AT335_002607, AT845_000732, B6R12_001779, B6R15_002614, BANRA_00209, BANRA_04745, BG944_002306, BHS81_22075, BJI68_21320, BJJ90_00020, BK292_20275, BMC79_001219, BMT49_22560, BMT91_10450, BN17_36471, BO068_002364, BOH76_09950, BON63_28245, BON64_05850, BON65_14475, BON67_01780, BON68_05285, BON70_16595, BON72_00895, BON73_15580, BON74_23700, BON75_21860, BON76_08970, BON77_20030, BON80_03735, BON81_25430, BON82_25325, BON83_15755, BON89_15000, BON93_02825, BON94_09555, BON95_10645, BON96_19205, BON97_19900, BON98_14605, BTQ06_07025, BvCmsF30A_02508, BvCmsHHP019_00330, BvCmsHHP056_04838, BvCmsKKP036_03000, BvCmsKKP061_01959, BVL39_07020, C2U48_14500, C3F40_17215, C5N07_22410, C5Y87_17685, C9114_09000, C9160_19130, C9E67_00260, CA593_07530, CCS08_08690, CDC27_20015, CG831_001056, CIG67_24645, CO706_17920, CR538_00020, CWS33_14860, CXJ73_004344, CY655_23555, D3822_07725, D3Y67_00315, D9D43_11505, D9D77_13480, D9E34_14670, D9H94_11280, D9J03_09540, DAH17_16135, DAH18_20125, DAH19_18090, DAH20_24220, DAH21_17525, DAH22_09920, DAH23_17915, DAH24_17880, DAH25_18135, DAH26_16750, DAH27_18385, DAH28_17575, DAH30_13775, DAH31_23190, DAH32_19355, DAH33_21850, DAH34_09310, DAH35_20475, DAH36_07260, DAH37_15165, DAH38_15235, DAH40_17235, DAH41_14365, DAH42_13695, DAH43_16215, DAH45_16595, DAH46_15435, DAH47_17090, DAH48_15825, DAH49_16905, DAH50_21850, DD762_09165, DEN88_13620, DEN89_16215, DEN90_12600, DEN91_23450, DEN92_12435, DEN93_08790, DEN94_10130, DEN95_14005, DEN96_09615, DEN97_10520, DEN98_07630, DEN99_11335, DEO00_06805, DEO02_16755, DEO03_14490, DEO12_11025, DEO13_12390, DEO14_23575, DEO15_11025, DEO17_22060, DEO18_15050, DEO19_13745, DEO20_16845, DIV22_14835, DN627_09770, DS732_26895, DTL43_15245, DTL90_16290, DTM45_17745, DXT69_21625, DXT71_06225, DXT73_04970, E2112_06345, E2113_08430, E2117_10350, E2119_14655, E2121_19695, E2122_13025, E2127_18200, E2128_05870, E2129_08165, E2131_06355, E2132_11120, E2133_16090, E2134_19510, E2135_07105, E4K51_15965, E5M02_07360, E5P22_08085, E5P23_15530, E5P24_21080, E5P25_17970, E5P26_09365, E5P27_17245, E5P28_10750, E5P29_05005, E5P30_22165, E5P31_14550, E5P32_04050, E5P35_11465, E5P36_07650, E5P37_10930, E5P39_09780, E5P40_09135, E5P41_11670, E5P42_10380, E5P43_11895, E5P44_15505, E5P45_10985, E5P46_05960, E5P47_15860, E5P48_08360, E5P49_08160, E5P50_10715, E5P51_07470, E5P52_21185, E5S34_11915, E5S35_10075, E5S36_12490, E5S38_13730, E5S42_10015, E5S43_10035, E5S45_08905, E5S47_13730, E5S48_08280, E5S51_11710, E5S53_07850, E5S55_06810, E5S56_16130, E5S57_15965, E5S61_13330, E5S62_14275, EAN77_14715, EAX79_08685, EBP16_13200, EC1094V2_4597, ED648_15945, EHD79_09375, EI021_09100, EIZ93_13665, EKI52_15115, EL79_0004, EL80_0004, ELT21_07915, ELT27_16490, ELT29_18730, ELT33_18135, ELT41_12100, ELU90_13065, ELU99_10295, ELV08_08920, ELV09_22460, ELV15_14380, ELV21_12600, ELV26_08235, ELV28_03740, ELX48_16725, ELX61_15160, ELX66_07175, ELX69_21520, ELX85_13995, ELX96_04430, ELY02_11060, ELY32_13970, ELY36_11305, ELY39_10885, ELY41_06090, ELY48_10375, EWK56_18880, EXX13_13520, EYV17_12765, EYV18_09145, EYX47_16120, F0L67_11425, F7F11_14145, F9B07_10285, F9S83_15510, F9V24_16795, F9X20_04280, FDM60_00555, FFF58_16645, FJQ51_13530, FKO60_15930, FOI11_017140, FOI11_06040, FQF29_14170, FV293_16155, FWK02_05940, FY127_10860, G4A38_07195, G9448_14990, GAJ26_15940, GF699_13160, GFY34_11620, GIB53_14670, GJ11_23670, GKF89_01630, GNZ05_16185, GQM09_08800, GQW68_08605, GRW05_18300, GSY44_14515, GUC01_19465, H0O72_09040, HI055_002025, HJS37_002371, HJU54_003666, HKA49_003820, HL563_13835, HMV95_19155, HNC36_11515, HNC66_20170, HV109_00020, HV209_21895, HVW19_21945, HVW43_16515, HVX16_00020, HVY77_00020, HVZ71_00020, HX136_00020, I6H00_18730, I6H01_12805, I6H02_14000, IA00_003393, IH768_12620, IH772_16375, J0541_001584, J5U05_002434, JE86ST02C_42510, JE86ST05C_42590, JFD_02858, JNP96_00020, NCTC10082_02399, NCTC10090_03099, NCTC11181_02322, NCTC11341_02415, NCTC12950_00005, NCTC4450_02049, NCTC8008_00160, NCTC8009_00855, NCTC8333_00039, NCTC8500_05706, NCTC8960_02654, NCTC9036_04954, NCTC9037_00256, NCTC9073_06496, NCTC9111_00438, NCTC9706_02311, NCTC9962_03132, ND22_002683, RG28_23775, SAMEA3472044_00586, SAMEA3472056_03737, SAMEA3472147_03622, SAMEA3751407_02407, SAMEA3752557_01205, SAMEA3753106_03244, TUM18780_00040, WP4S18E07_00040, WR15_16325 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for C3SLN3 (Escherichia coli) Explore C3SLN3 Go to UniProtKB: C3SLN3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C3SLN3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B46 Query on B46 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	prop-2-yn-1-yl {[5-(4-piperidin-1-yl-2-pyridin-3-yl-1,3-thiazol-5-yl)-1H-pyrazol-3-yl]methyl}carbamate C₂₁ H₂₂ N₆ O₂ S DJDJEDRAXXHMHQ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.234
R-Value Work: 0.206
R-Value Observed: 0.208
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.4	α = 90
b = 95.4	β = 90
c = 51.25	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-02-09

Deposition Author(s):

Wei, Y.

Charifson, P.

Revision History (Full details and data files)

Version 1.0: 2010-02-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-07-03
Changes: Database references
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description