PDB-9r0y: Crystal structure of NDM-1 with thiol compound 22b

ID or keywords:

Entry

Database: PDB / ID: 9r0y

Title

Crystal structure of NDM-1 with thiol compound 22b

Components

Metallo-beta-lactamase type 2

Keywords

ANTIMICROBIAL PROTEIN / inhibitor / thiol / antimicrobial resistance / metall-beta-lactamase

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.27 Å

Authors

Hinchliffe, P. / Spencer, J.

Funding support

European Union, 1items

Citation

Journal: Eur J Med Chem Rep / Year: 2025
Title: Repurposing of compound libraries yields new inhibitors of NDM-1 metallo-beta-lactamase with diverse zinc-binding moieties
Authors: Kavas, V. / Hinchliffe, P. / Zorman, M. / Krajnc, A. / Proj, M. / Golob, M. / Rambaher, M.H. / Spencer, J. / Gobec, S.

History

Deposition	Apr 24, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 9, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9r0y.cif.gz	328.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9r0y.ent.gz		Display	PDB format
PDBx/mmJSON format	9r0y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9r0y_validation.pdf.gz	976.6 KB	Display	wwPDB validaton report
Full document	9r0y_full_validation.pdf.gz	981.5 KB	Display
Data in XML	9r0y_validation.xml.gz	26.8 KB	Display
Data in CIF	9r0y_validation.cif.gz	38 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r0/9r0y ftp://data.pdbj.org/pub/pdb/validation_reports/r0/9r0y	HTTPS FTP

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Related structure data

Related structure data	9r0xC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (4) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Metallo-beta-lactamase type 2

B: Metallo-beta-lactamase type 2

hetero molecules

52.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	68.383, 73.350, 76.955
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1 Mass: 26045.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7C422, beta-lactamase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-A1JCK / ~{N}-naphthalen-2-yl-2-sulfanyl-ethanamide / SGMHGVVTMOGJMX-UHFFFAOYSA-N Mass: 217.287 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₁₁NOS / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.85 Å³/Da / Density % sol: 33.6 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 0.1M bis-tris pH 5.8, 32% PEG 3350, 0.15M (NH4)2SO4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9405 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 28, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9405 Å / Relative weight: 1
Reflection	Resolution: 1.27→53.1 Å / Num. obs: 101950 / % possible obs: 99.5 % / Redundancy: 13.4 % / B_iso Wilson estimate: 15.1 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.037 / Net I/σ(I): 9.7
Reflection shell	Resolution: 1.27→1.29 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4949 / CC_1/2: 0.27 / R_pim(I) all: 0.892

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
DIALS		data reduction
DIALS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.27→50.02 Å / SU ML: 0.1779 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.0278
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1912	1965	1.93 %
R_work	0.1655	99756	-
obs	0.166	101721	99.28 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 21.76 Å²

Refinement step

Cycle: LAST / Resolution: 1.27→50.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3416	0	39	472	3927

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0073	3626
X-RAY DIFFRACTION	f_angle_d	1.0034	4956
X-RAY DIFFRACTION	f_chiral_restr	0.0833	544
X-RAY DIFFRACTION	f_plane_restr	0.0087	675
X-RAY DIFFRACTION	f_dihedral_angle_d	11.995	1286

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.27-1.3	0.3273	116	0.3487	6952	X-RAY DIFFRACTION	97.69
1.3-1.34	0.3716	159	0.3465	7014	X-RAY DIFFRACTION	99.13
1.34-1.38	0.3399	143	0.3169	7041	X-RAY DIFFRACTION	99.24
1.38-1.42	0.3398	125	0.2936	6996	X-RAY DIFFRACTION	98.23
1.42-1.47	0.2764	169	0.2584	7059	X-RAY DIFFRACTION	99.7
1.47-1.53	0.2546	133	0.2337	7096	X-RAY DIFFRACTION	99.81
1.53-1.6	0.2229	154	0.2034	7120	X-RAY DIFFRACTION	99.97
1.6-1.68	0.1994	152	0.1765	7129	X-RAY DIFFRACTION	99.99
1.68-1.79	0.1902	149	0.1579	7155	X-RAY DIFFRACTION	99.89
1.79-1.93	0.1943	123	0.1527	7053	X-RAY DIFFRACTION	98.19
1.93-2.12	0.1849	133	0.1408	7180	X-RAY DIFFRACTION	99.84
2.12-2.43	0.1761	107	0.1326	7250	X-RAY DIFFRACTION	99.73
2.43-3.06	0.1599	127	0.1387	7293	X-RAY DIFFRACTION	99.95
3.06-50.02	0.157	175	0.139	7418	X-RAY DIFFRACTION	98.58

Refinement TLS params.

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

ID	L11 (°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)
1	4.2180668857	-4.18426568053	-5.85138447849	7.93468571772	4.25631517155	9.15913149241	-0.346373495682	-0.365981833295	-0.283586545701	0.314887433369	0.303264292196	-0.214157546755	0.688780459411	0.351432944469	0.0681967859774	0.193270944906	-0.00179066038303	-0.0104825422253	0.105637901538	0.0168345130138	0.157212518816	15.2402780984	-13.6213611528	22.5504639917
2	3.80930998973	-0.0422880373812	0.118572744904	2.11760636606	0.285835303577	2.35123580352	-0.0351111404168	0.0165490506646	-0.250710455734	-0.00997663743702	0.0492256285397	-0.1353908156	0.187738113716	0.126359791202	-0.00795836447159	0.113365805456	0.0084741396611	0.00454019932281	0.0746318278189	-0.0046976376554	0.0911931835058	16.8608975787	-8.50074256217	15.9154830677
3	0.833597137529	0.0773589978959	-0.257107022718	2.41520881422	0.400895550031	1.05535038266	0.0124325715067	0.0618466256309	0.00364245418745	-0.07187733471	0.00163701847981	0.0143520809168	-0.0102763187719	-0.0740150800105	-0.0160252258154	0.0838837474012	-0.00627081011238	-0.00921020822522	0.112173021054	0.0100859859213	0.0749795070132	12.720720729	5.06874819294	10.9758645256
4	0.600196583525	-0.051835304383	0.503212985851	2.62334106219	-0.431802798024	2.25489468046	-0.0437360919918	-0.0521102515015	-0.0170044382496	0.0578885860308	-0.0383916604555	-0.239199114715	-0.0392161572563	0.169780306387	0.112155021771	0.086940778887	0.00791768065608	0.00187474448265	0.131737680998	0.00769150750753	0.0894082446863	18.7246498026	8.57501778083	25.3562214348
5	0.617289441069	-1.57200998376	0.644389765707	6.38223684175	-1.14293437577	5.01075110492	-0.0791073751391	-0.286065998213	-0.200936095927	0.163118565552	0.178830711171	0.169436347806	0.000462686288535	-0.0686181928822	-0.0695835744364	0.0993603345165	-0.015302603193	-0.0201648436998	0.139265251408	0.0150306227052	0.0872440541587	14.8360695813	1.63312629809	28.8330482369
6	8.59703165671	5.81432438499	-2.7459207123	4.53272821288	-2.93681365564	7.68232127629	0.201717047918	-0.0209021618313	0.1157185696	0.356296464948	-0.145857125173	-0.191534742619	-0.418729294964	0.511043317457	0.0192773780756	0.150048521485	-0.00327096130828	-0.0117883240303	0.157993131158	0.00859891132367	0.119331982179	22.6715677148	12.7815555822	32.1625776663
7	1.75159523679	-1.38916999693	-0.833012774025	3.08670969073	2.77421441211	2.95736696987	0.132660601269	0.0850079679836	0.605174822874	-0.259784734218	0.215960109469	-0.724370776218	-0.823322397885	0.652533471475	-0.263998195582	0.324896797333	-0.0512034881562	0.0479747934335	0.215377394281	0.0136134998736	0.349518518136	20.9034160824	48.8988777202	2.19594487101
8	7.10331689647	-0.447825068599	4.90755673323	3.46372721825	0.111705098149	7.35125992928	-0.0595217149216	-0.258913534862	0.254744216222	0.401367661517	0.0405928929002	-0.643398510735	-0.0958560979612	0.318224415854	0.0805874319288	0.186409832751	-0.0119674930371	-0.0490060396483	0.159958199277	-0.0139737043704	0.276677899741	24.7141001531	42.6065653039	11.7135729027
9	4.50939625939	-0.934252087163	3.01275911834	2.85154176735	-0.0979274045936	4.91012165742	0.00751045846483	0.0982237838169	0.268626036805	-0.038233284239	-0.0610274534025	-0.0778367788602	-0.0498030007694	0.0580332532989	-0.0970920039613	0.0913961992937	-0.00641582170815	0.014301533738	0.0746074704352	-0.00018833007637	0.111952132595	15.5184914113	39.7931018115	5.98881192436
10	6.40403963128	-2.03832472036	3.6522734654	5.48534768196	-1.62666835548	7.18791443642	-0.292046837616	-0.0735144713359	0.401792301135	0.160817427612	0.0477617831105	-0.159683262632	-0.615888198789	-0.14744682363	0.329017029559	0.166708268026	0.0053450839055	-0.00786172360636	0.104896240094	-0.0234755241268	0.170723570562	12.2498659487	48.0903751943	10.1443434043
11	0.612232293137	-0.603464675537	-0.0979295089576	4.18184673262	0.298724829589	0.595082893071	-0.0215769607614	-0.0323369891904	0.0187577280007	0.171702073164	0.0119515486607	0.0870459003928	-0.0341578831532	-0.0465678302855	0.0149240702467	0.0862561322575	0.00569871764133	0.00985738844995	0.119616975114	0.00358520019676	0.113700072816	10.9285129177	30.5881577729	11.4118615544
12	5.94555278315	-0.851295644845	2.37939685581	3.20055632989	-0.724877978945	4.60442190124	0.0276446488385	0.0251138409057	-0.0473545743957	-0.0852365386081	-0.022892147164	0.132876484163	0.0192236939672	-0.0818043689062	-0.0164572266791	0.0756922132634	-0.0082429584	0.0226224865427	0.0584742132031	-0.012324699482	0.106117900234	14.390027731	24.8166657294	4.64059466977
13	1.99563123179	-0.735234403233	0.134913362332	2.17359308522	-1.35470626154	2.17338066944	0.0377205428889	0.032330802796	0.0703150233696	0.0367940904301	-0.0634058322782	-0.149758901799	-0.0965378017403	0.24263364308	0.0121687244112	0.107474472916	-0.0158362078323	0.014848487057	0.160089387817	-0.0210785953925	0.147611944065	26.931771346	28.0588136921	5.52595236569
14	1.88730597149	0.225773023986	0.635948541344	5.23834351517	-0.61095083622	2.49407191347	-0.0115011488278	0.0598695490474	0.0929670917822	-0.191639218476	-0.043389470936	-0.0288298742938	-0.025649970901	0.168391096612	0.0515480243938	0.0760567107926	0.00585750644833	0.0441013067226	0.162758815355	0.00203642863081	0.137714285806	26.2165220302	28.7286352064	-0.733176598437
15	7.54495348009	-2.83928728746	3.55142068248	5.61115654763	-4.92904406794	8.15757570695	0.156172036382	-0.0146550030813	-0.201178153317	-0.0759424801726	-0.281513133915	-0.244238216905	0.261896372473	0.643633796663	0.168610725914	0.143656828066	0.0292338394338	0.045436172492	0.218440833693	0.00306086115887	0.212488646545	34.834061522	23.3674634686	2.67428200868

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 43 through 57 )	A	A	43 - 57	1 - 15
2	2	chain 'A' and (resid 58 through 108 )	A	A	58 - 108	16 - 66
3	3	chain 'A' and (resid 109 through 194 )	A	A	109 - 194	67 - 152
4	4	chain 'A' and (resid 195 through 239 )	A	A	195 - 239	153 - 197
5	5	chain 'A' and (resid 240 through 255 )	A	A	240 - 255	198 - 213
6	6	chain 'A' and (resid 256 through 270 )	A	A	256 - 270	214 - 228
7	7	chain 'B' and (resid 40 through 57 )	B	F	40 - 57	1 - 18
8	8	chain 'B' and (resid 58 through 70 )	B	F	58 - 70	19 - 31
9	9	chain 'B' and (resid 71 through 94 )	B	F	71 - 94	32 - 55
10	10	chain 'B' and (resid 95 through 108 )	B	F	95 - 108	56 - 69
11	11	chain 'B' and (resid 109 through 170 )	B	F	109 - 170	70 - 131
12	12	chain 'B' and (resid 171 through 194 )	B	F	171 - 194	132 - 155
13	13	chain 'B' and (resid 195 through 228 )	B	F	195 - 228	156 - 189
14	14	chain 'B' and (resid 229 through 255 )	B	F	229 - 255	190 - 216
15	15	chain 'B' and (resid 256 through 270 )	B	F	256 - 270	217 - 231

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