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- PDB-7up3: NDM1-inhibitor co-structure -

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Basic information

Entry
Database: PDB / ID: 7up3
TitleNDM1-inhibitor co-structure
ComponentsMetallo beta-lactamase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Metallo-beta-lactamase inhibitor / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / metal ion binding
Similarity search - Function
Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
: / Chem-NZ0 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsScapin, G. / Fischmann, T.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Rapid Evolution of a Fragment-like Molecule to Pan-Metallo-Beta-Lactamase Inhibitors: Initial Leads toward Clinical Candidates.
Authors: Mandal, M. / Xiao, L. / Pan, W. / Scapin, G. / Li, G. / Tang, H. / Yang, S.W. / Pan, J. / Root, Y. / de Jesus, R.K. / Yang, C. / Prosise, W. / Dayananth, P. / Mirza, A. / Therien, A.G. / ...Authors: Mandal, M. / Xiao, L. / Pan, W. / Scapin, G. / Li, G. / Tang, H. / Yang, S.W. / Pan, J. / Root, Y. / de Jesus, R.K. / Yang, C. / Prosise, W. / Dayananth, P. / Mirza, A. / Therien, A.G. / Young, K. / Flattery, A. / Garlisi, C. / Zhang, R. / Chu, D. / Sheth, P. / Chu, I. / Wu, J. / Markgraf, C. / Kim, H.Y. / Painter, R. / Mayhood, T.W. / DiNunzio, E. / Wyss, D.F. / Buevich, A.V. / Fischmann, T. / Pasternak, A. / Dong, S. / Hicks, J.D. / Villafania, A. / Liang, L. / Murgolo, N. / Black, T. / Hagmann, W.K. / Tata, J. / Parmee, E.R. / Weber, A.E. / Su, J. / Tang, H.
History
DepositionApr 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo beta-lactamase
B: Metallo beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,29713
Polymers52,5892
Non-polymers1,70811
Water5,603311
1
A: Metallo beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0306
Polymers26,2951
Non-polymers7355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2687
Polymers26,2951
Non-polymers9736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.564, 73.913, 77.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallo beta-lactamase / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase / NDM-1 / Metallobetalactamase NDM-1 / NDM1 ...Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase / NDM-1 / Metallobetalactamase NDM-1 / NDM1 metallo-beta-lactamase / New Delhi Metallo carbapenemase-1 / New Delhi metallo beta lactamase 1 / New Delhi metallo-beta-lactamase NDM-1 / Subclass B1 metallo-beta-lactamase NDM-1


Mass: 26294.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: blaNDM-1, bla NDM-1, blaNDM1, NDM-1, D647_p47098, DDJ63_29735, EC13450_007, NCTC13443_00040, p2146_00143, pCRE380_21, pN11x00042NDM_090, pNDM-SX04_5, pNDM10469_138, SAMEA3499901_05193, TR3_031, TR4_031
Production host: Escherichia coli (E. coli) / References: UniProt: E9NWK5

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Non-polymers , 5 types, 322 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NZ0 / (3P)-4-[4-(hydroxymethyl)phenyl]-3-(2H-tetrazol-5-yl)pyridine-2-sulfonamide


Mass: 332.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N6O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium acetate 1.0 mM TCEP 3.0 mM cadmium sulfate 0.1 M HEPES pH 7.0 25.0 w/v polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.113→134.175 Å / Num. all: 163291 / Num. obs: 163291 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 17.2 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.105 / Rsym value: 0.094 / Net I/av σ(I): 5.9 / Net I/σ(I): 18 / Num. measured all: 2088252
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value
1.113-1.1712.60.5621.4235380.1710.6120.562
1.17-1.2412.20.4471.7223770.1390.4890.447
1.24-1.33130.3392.2210230.1020.3690.339
1.33-1.4412.70.243.1196160.0730.2630.24
1.44-1.5713.10.1634.6181130.050.180.163
1.57-1.7613.40.1146.5164180.0350.1270.114
1.76-2.0312.70.0779.1145350.0250.0880.077
2.03-2.4913.20.05911.4123700.0190.0680.059
2.49-3.5212.50.04812.597180.0160.0560.048
3.52-134.17512.50.04413.455830.0140.050.044

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALA3.3.20data scaling
PDB_EXTRACT3.27data extraction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3ZR9

3zr9


Resolution: 1.4→31.72 Å / Cor.coef. Fo:Fc: 0.9434 / Cor.coef. Fo:Fc free: 0.9418 / SU R Cruickshank DPI: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.061 / SU Rfree Cruickshank DPI: 0.06
RfactorNum. reflection% reflectionSelection details
Rfree0.1899 3839 5.02 %RANDOM
Rwork0.1803 ---
obs0.1808 76421 96.65 %-
Displacement parametersBiso max: 106.58 Å2 / Biso mean: 23.06 Å2 / Biso min: 10.04 Å2
Baniso -1Baniso -2Baniso -3
1--4.8733 Å20 Å20 Å2
2--3.8472 Å20 Å2
3---1.0261 Å2
Refine analyzeLuzzati coordinate error obs: 0.171 Å
Refinement stepCycle: final / Resolution: 1.4→31.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 68 311 3760
Biso mean--30.13 28.95 -
Num. residues----458
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1138SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes540HARMONIC5
X-RAY DIFFRACTIONt_it3536HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion465SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4312SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3536HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4825HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion4.13
X-RAY DIFFRACTIONt_other_torsion16.09
LS refinement shellResolution: 1.4→1.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1977 255 5.02 %
Rwork0.1932 4827 -
all0.1934 5082 -
obs--96.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.66390.0749-0.02683.3249-0.3570.40840.0219-0.012-0.09150.4622-0.0708-0.10950.00480.02440.0489-0.0101-0.0097-0.0221-0.06990.004-0.0869-16.18323.3328-5.7768
20.3459-0.08860.10291.5731-0.00570.6734-0.00840.01580.04390.0388-0.0191-0.0282-0.04050.00520.0275-0.03010.0021-0.0029-0.01180.0076-0.0468-18.821535.6515-18.0533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A42 - 269
2X-RAY DIFFRACTION2{ B|* }B42 - 270

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