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


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


This is version 1.2 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

  • DOI: 10.1016/j.bmcl.2010.03.052
  • Structures With Same Primary Citation

  • 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 c ...

    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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
A
203Escherichia coliMutation(s): 0 
Gene Names: 
ECs4634gyrBA6581_09865A6592_18480A6V01_14135A8C65_04830A9819_21235A9R57_11890A9X72_00020AC789_1c40830ACN002_3797ACN68_13005ACN81_06740ACU57_14935ACU90_00535AM464_11760AMK83_17235AML07_02225AML35_24145APT94_09995ARC77_15395AU473_02465AUQ13_22835AUS26_01355AW106_07345AWB10_00020BANRA_02361BANRA_03254BANRA_04568BANRA_04745BB545_21370BHF03_11525BHS81_22075BHS87_20785BJJ90_00020BK292_20275BK296_18275BK375_10440BMA87_08950BMT49_22560BMT91_10450BN17_36471BOH76_09950BON63_28245BON65_14475BON72_00895BON75_21860BON76_08970BON83_15755BON94_09555BON95_10645BON96_19205BTQ04_21185BTQ06_07025BUE81_08910BvCms12BK_01711BvCms2454_00319BvCms28BK_02451BvCms35BK_04075BvCmsC61A_04456BvCmsHHP001_00491BvCmsHHP019_00330BvCmsHHP056_04838BvCmsKKP036_03000BvCmsKKP061_01959BvCmsKSNP120_03356BvCmsKSP011_01328BvCmsKSP024_04447BvCmsKSP026_00219BvCmsKSP045_03951BvCmsKSP058_02724BvCmsKSP067_00519BvCmsKSP076_00383BvCmsNSNP036_04824BvCmsNSP006_02118BvCmsNSP007_02966BvCmsNSP047_02734BvCmsNSP072_01227BvCmsOUP014_00224BvCmsSINP011_01209BvCmsSINP022_00622BvCmsSIP019_04120BvCmsSIP044_03951BVL39_07020BW690_02000BWP17_17165BZL31_10210C2U48_14500C5715_00865C5N07_22410C5P01_14605C5P44_14220C6669_09190C7235_00020C7B02_15315C7B06_18340C7B07_18330C7B08_22750C7B18_21110C9098_19090C9114_09000C9141_17480C9160_19130C9162_15850C9201_16730C9306_10445C9E25_06660C9E67_00260C9Z03_00990C9Z23_09685C9Z28_22890C9Z29_14965C9Z37_12950C9Z39_08880C9Z43_17085C9Z89_12855CA593_07530CDC27_20015CF006_10825CG692_02240CI641_011820CI693_04540CI694_10210CIG45_21285CJU63_21960CJU64_22080CMR93_16945CO706_17920COD30_14315COD46_05340CR538_00020CRD98_06155CRE06_17215CRM83_20215CVH05_01450CWS33_14860D2184_13215D2185_10575D3821_17540D3822_07725D3O91_05925D3Y67_00315D4011_10415D4023_13630D4074_11320D4628_10290D4638_19055D4660_11830D4718_16555D4L91_08755D4M06_08575D4U85_12295D5H35_02745D5I97_17305D6004_02645D6C36_11460D6D43_12690D6T60_12980D6T98_06565D6W00_19015D6X36_14150D6X63_17215D6X76_16010D7K33_13470D7K63_14370D7K66_11005D7W70_03620D8Y65_17090D9610_01545D9C99_01865D9D20_14880D9D31_09440D9D43_11505D9D44_13360D9D94_18355D9E34_14670D9E35_19195D9F87_21805D9G29_12785D9G48_06470D9G69_23320D9G95_12510D9H53_15275D9H68_11910D9H70_07770D9H94_11280D9I18_07845D9I88_05665D9I97_14535D9J03_09540D9J11_15665D9J44_15390D9J46_01915D9J52_17035D9J78_11620D9K48_06220D9K54_22005D9L89_14400D9S45_11600D9X77_10720D9X97_19780D9Z28_04785DAH18_20125DAH26_16750DAH30_13775DAH32_19355DAH34_09310DAH37_15165DAH43_16215DBQ99_01225DD762_09165DEN89_16215DEN97_10520DEO19_13745DIV22_14835DJ503_03740DL292_08710DL326_20015DL455_13395DL479_05540DL530_06300DL545_00020DL705_04180DL800_26075DL979_08705DLT82_05815DLU50_05595DLU67_12080DLU82_10995DLW60_08205DLW88_11480DLX40_10585DLY41_02550DLY44_14815DM102_20425DM155_02680DM267_09210DM296_12830DM382_02225DM962_09845DM973_13100DMI04_10430DMI53_10720DMO02_12015DMY83_11985DN627_09770DN703_10995DN808_05135DNB37_13135DNC98_03220DNI21_06120DNJ62_13385DNK12_11565DNR35_14990DNW42_09690DNX19_06145DOE35_09915DOS18_10495DOT81_11585DOU81_09005DOY22_14770DOY56_10965DOY61_14810DP258_15855DP265_03520DP277_10840DQE83_08455DQE91_13285DQF36_07740DQF57_16010DQF71_07875DQF72_06050DQG35_14175DQP61_05880DRP48_11930DS143_08110DS721_09030DS732_26895DS966_11265DT034_13610DTL43_15245DTL90_16290DTM45_17745DTZ20_11700DVB38_01615DXT69_21625DXT71_06225DXT73_04970DXX80_012545E0K84_08990E2112_06345E2119_14655E2127_18200E2128_05870E2129_08165E2134_19510E2135_07105E2855_04697E2863_04385E4K55_18705E4K60_17945E4K61_17455E5P22_08085E5P28_10750E5P37_10930E5S42_10015E5S47_13730E5S61_13330EA213_16110EA214_17495EAI52_06640EAM59_18785EAN70_12550EAN77_14715EAX79_08685EB476_12385EB509_13420EB510_17625EB515_14425EBA84_13540EBJ06_18375EBM08_01505EC1094V2_4597EC3234A_68c00420EC3426_04870EC382_17790ECTO6_00004ED225_21960ED307_04470ED600_09065ED607_13695ED611_15795ED648_15945ED903_12480ED944_14870EEA45_18020EEP23_06945EF173_14940EG075_16865EG599_08615EG796_06995EG808_05530EGC26_20465EGU87_10255EH186_05705EHD63_17780EHD79_09375EHH55_27215EHJ66_15495EHV90_11450EHW09_15610EHX09_10490EI021_09100EI028_20140EI032_04900EIA21_14370EIZ86_16545EIZ93_13665EJ366_23390EJC75_18105EKI52_15115EL75_0004EL79_0004EL80_0004ELT33_18135ELV08_08920ELV15_14380ELV28_03740ELY05_09195EO241_19880EPT01_03925EQ820_07760EQ823_16820ERS085365_03612ERS085366_02215ERS085374_02710ERS085379_02346ERS085383_02572ERS085386_02495ERS085404_03525ERS139211_01417ERS150876_02109EST51_00020EVY14_14630EWK56_18880EXM29_08070EXX06_15155EXX13_13520EXX23_18050EXX24_15275EXX53_14100EXX55_16850EXX71_19825EXX78_09055EXX87_23415EYD11_00020EYY34_05560F1E13_14725F1E19_19945F7F00_12565F7F11_14145F7F18_08965F7F23_11930F7F26_18050F7F29_10500F7G01_11790F7G03_18095F9Z74_13265FAF34_000945FE846_12230FKO60_15930FORC82_0004FQ022_10415FQ915_15675FQR64_00440FQZ46_08085FRV13_17740FV293_16155FV438_15390FWK02_05940FY127_10860GHR40_05000GII67_11760GIY19_17290GJ11_23670GJD97_00020GKF74_17465GKF86_19015GKF89_01630GKG12_12975GN312_09520GNZ03_19680GP654_17235GP661_13635GP664_08990GP666_17955GP689_18070GP720_16250GP935_15515GP946_01910GP950_07065GQE22_09685GQE30_12635GQE34_04380GQE42_15400GQE51_13990GQE64_10800GQE68_16375GQE88_11760GQM09_08800GQM17_18690GRW42_15395GRW80_05235HmCms184_02305HmCmsJML074_02035HW43_23415NCTC10082_02399NCTC10090_03099NCTC10963_00010NCTC11022_03933NCTC11181_02322NCTC11341_02415NCTC12650_00281NCTC12950_00005NCTC8009_00855NCTC8500_05706NCTC8960_02654NCTC9036_04954NCTC9055_01972NCTC9062_03106NCTC9073_06496NCTC9111_00438NCTC9119_00034NCTC9701_00107NCTC9703_04528NCTC9706_02311NCTC9962_03132NCTC9969_00215PGD_00276PU06_20825RG28_23775RK56_018895RX35_03549SAMEA3472043_04198SAMEA3472044_00586SAMEA3472047_02680SAMEA3472056_03737SAMEA3472070_04115SAMEA3472080_03431SAMEA3472108_02463SAMEA3472110_03292SAMEA3472112_02380SAMEA3472114_04240SAMEA3472147_03622SAMEA3484427_03608SAMEA3484429_03609SAMEA3484434_01312SAMEA3485101_04068SAMEA3485113_02781SAMEA3752372_03470SAMEA3752557_01205SAMEA3752559_02472SAMEA3753064_04237SAMEA3753097_00947SAMEA3753290_04459SAMEA3753300_03007SK85_04028UC41_07835UN86_05880UN91_09725WQ89_11080WR15_16325

EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
Find proteins for C3SLN3 (Escherichia coli)
Go to UniProtKB:  C3SLN3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B46
Query on B46

Download CCD File 
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
 Ligand Interaction
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 = 95.4α = 90
b = 95.4β = 90
c = 51.25γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History 

  • 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