4L0L

Crystal structure of P.aeruginosa PBP3 in complex with compound 4

• PDB DOI:  https://doi.org/10.2210/pdb4L0L/pdb

• Classification: Penicillin Binding Protein/Antibiotic
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-31 Released: 2013-08-21 
• Deposition Author(s): Han, S., Marr, E.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.275 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Literature

Pyridone-conjugated monobactam antibiotics with gram-negative activity.

Brown, M.F., Mitton-Fry, M.J., Arcari, J.T., Barham, R., Casavant, J., Gerstenberger, B.S., Han, S., Hardink, J.R., Harris, T.M., Hoang, T., Huband, M.D., Lall, M.S., Lemmon, M.M., Li, C., Lin, J., McCurdy, S.P., McElroy, E., McPherson, C., Marr, E.S., Mueller, J.P., Mullins, L., Nikitenko, A.A., Noe, M.C., Penzien, J., Plummer, M.S., Schuff, B.P., Shanmugasundaram, V., Starr, J.T., Sun, J., Tomaras, A., Young, J.A., Zaniewski, R.P.

(2013) J Med Chem 56: 5541-5552

• PubMed: 23755848 
• DOI: https://doi.org/10.1021/jm400560z
• Primary Citation of Related Structures:  
  4L0L


• PubMed Abstract: 
  

  Herein we describe the structure-aided design and synthesis of a series of pyridone-conjugated monobactam analogues with in vitro antibacterial activity against clinically relevant Gram-negative species including Pseudomonas aeruginosa , Klebsiella pneumoniae , and Escherichia coli . Rat pharmacokinetic studies with compound 17 demonstrate low clearance and low plasma protein binding. In addition, evidence is provided for a number of analogues suggesting that the siderophore receptors PiuA and PirA play a role in drug uptake in P. aeruginosa strain PAO1.

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Organizational Affiliation: 

Worldwide Medicinal Chemistry, ‡Computational Chemistry, §Antibacterials Research Unit, ∥Pharmacokinetics, Dynamics & Metabolism, ⊥Structural Biology, Pfizer Global Research and Development , Eastern Point Road, Groton, Connecticut 06340, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.83 kDa 
• Atom Count: 4,120 
• Modelled Residue Count: 501 
• Deposited Residue Count: 537 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 3	A	537	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names:  pbpB, ftsI, ftsI1, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, E4V10_06485, E5Z62_07090, E5Z63_09665, ECC04_026610, GNQ48_11285, GUL26_13375, IPC111_21940, IPC112_19015, IPC116_09585, IPC117_07395, IPC118_04920, IPC119_07395, IPC120_15550, IPC121_09095, IPC122_04780, IPC124_14230, IPC125_21870, IPC126_24180, IPC127_12935, IPC128_22805, IPC1295_15535, IPC129_24365, IPC1306_24915, IPC1308_23220, IPC1309_06985, IPC130_24445, IPC1311_16270, IPC1312_15480, IPC1313_17325, IPC1315_21965, IPC1316_24135, IPC1317_23495, IPC1318_09915, IPC1319_09685, IPC1320_11910, IPC1321_25630, IPC1322_16515, IPC1323_21620, IPC1324_17780, IPC1328_23340, IPC1329_22455, IPC1330_20130, IPC1331_17140, IPC1333_25770, IPC1334_18700, IPC1336_22140, IPC1337_16335, IPC1339_21875, IPC133_15090, IPC1340_16145, IPC1342_14215, IPC1343_11535, IPC1345_18495, IPC1346_17840, IPC1348_23430, IPC1349_28020, IPC135_19275, IPC137_16810, IPC139_13895, IPC140_17455, IPC144_23880, IPC145_17255, IPC146_16795, IPC1474_21360, IPC1476_21625, IPC1477_15000, IPC1478_19345, IPC1479_03825, IPC147_20975, IPC1480_19760, IPC1481_11065, IPC1482_17070, IPC1485_22740, IPC1486_17305, IPC148_23485, IPC1491_10310, IPC1492_18840, IPC1494_20745, IPC1495_16885, IPC1496_18835, IPC1498_22375, IPC1499_03665, IPC149_19690, IPC1500_25120, IPC1501_27240, IPC1502_22370, IPC1503_25385, IPC1504_21360, IPC1505_04040, IPC1506_20465, IPC1507_10470, IPC1508_21520, IPC1509_19770, IPC150_20385, IPC1510_17840, IPC1511_21000, IPC1512_13610, IPC1513_16690, IPC1514_20090, IPC1515_10850, IPC1516_13270, IPC1517_24555, IPC1518_01875, IPC1519_14090, IPC151_19655, IPC1520_22790, IPC1522_10310, IPC1523_17450, IPC152_11895, IPC1584_03775, IPC1585_15345, IPC1587_21565, IPC1589_28245, IPC1591_18430, IPC1596_21245, IPC1597_23430, IPC1598_08735, IPC1600_19810, IPC1601_18255, IPC1602_14680, IPC1603_16790, IPC1605_28380, IPC1606_28410, IPC161_22390, IPC162_22765, IPC163_25155, IPC164_25610, IPC165_24935, IPC166_24030, IPC167_24555, IPC169_24955, IPC170_23205, IPC171_23005, IPC172_17205, IPC173_11420, IPC174_18480, IPC176_25775, IPC177_15180, IPC178_25080, IPC179_16825, IPC180_12965, IPC181_21340, IPC182_21690, IPC183_11825, IPC27_13015, IPC29_19575, IPC31_15495, IPC32_12355, IPC37_20205, IPC38_24330, IPC40_17705, IPC43_17085, IPC44_18585, IPC45_16465, IPC48_18610, IPC54_25285, IPC55_22610, IPC56_09545, IPC574_19200, IPC575_21310, IPC576_20080, IPC577_15555, IPC578_27125, IPC579_26205, IPC57_10695, IPC580_18590, IPC582_20545, IPC584_24515, IPC586_22885, IPC589_22365, IPC58_16175, IPC596_25775, IPC597_20615, IPC598_25385, IPC599_19915, IPC59_14695, IPC600_21820, IPC601_19795, IPC602_17520, IPC603_15045, IPC604_26500, IPC605_16140, IPC606_14030, IPC607_25595, IPC608_14115, IPC609_21275, IPC60_13915, IPC610_06665, IPC611_20380, IPC612_23580, IPC613_12215, IPC614_11190, IPC615_18845, IPC616_20660, IPC618_04580, IPC61_22670, IPC620_22215, IPC621_20220, IPC622_19205, IPC623_10250, IPC624_27490, IPC625_24025, IPC627_20940, IPC629_18305, IPC630_16550, IPC632_20610, IPC633_21150, IPC634_22690, IPC64_21390, IPC67_11930, IPC68_07130, IPC72_15035, IPC737_20650, IPC73_21415, IPC74_23890, IPC75_23210, IPC76_18105, IPC77_02350, IPC78_21830, NCTC13621_04221, PA52Ts2_1506 EC: 3.4.16.4
UniProt
Find proteins for Q51504 (Pseudomonas aeruginosa) Explore Q51504  Go to UniProtKB:  Q51504

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PFV	B [auth A]	(6R,7S,10Z)-10-(2-amino-1,3-thiazol-4-yl)-1-(1,5-dihydroxy-4-oxo-1,4-dihydropyridin-2-yl)-7-formyl-13,13-dimethyl-3,9-dioxo-6-(sulfoamino)-12-oxa-2,4,8,11-tetraazatetradec-10-en-14-oic acid C20 H26 N8 O12 S2 DRGQACYRFXBYPT-SATPWBBZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PFV	PDBBind:  4L0L	IC50: 54 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.275 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.725	α = 90
b = 82.832	β = 90
c = 88.689	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Han, S., Marr, E.S.

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2014-01-22
  Changes: Database references