PDB-9bnr: 4-(2-isothiocyanatoethyl)benzenesulfonamide complexed with Macrop...

ID or keywords:

Entry

Database: PDB / ID: 9bnr

Title

4-(2-isothiocyanatoethyl)benzenesulfonamide complexed with Macrophage Migration Inhibitory Factor

Components

Macrophage migration inhibitory factor

Keywords

ISOMERASE / CYTOKINE / TAUTOMERASE / ISOTHIOCYANATE / ISOMERASE INHIBITOR COMPLEX

Function / homology

Function and homology information

positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / carboxylic acid metabolic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / negative regulation of protein metabolic process / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / positive regulation of protein kinase A signaling / protein homotrimerization / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / positive regulation of phosphorylation / positive regulation of B cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / positive regulation of cytokine production / cytokine activity / Cell surface interactions at the vascular wall / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / vesicle / ficolin-1-rich granule lumen / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.53 Å

Authors

Fellner, M. / Rutledge, M.T. / Putha, L. / Kok, L.K. / Gamble, A.B. / Wilbanks, S.M. / Vernall, A.J. / Tyndall, J.D.A.

Funding support

1items

Citation

Journal: Chemmedchem / Year: 2024
Title: Covalent isothiocyanate inhibitors of macrophage migration inhibitory factor as potential colorectal cancer treatments.
Authors: Tyndall, J. / Putha, L. / Kok, L.K. / Fellner, M. / Rutledge, M.T. / Gamble, A.B. / Wilbanks, S.M. / Vernall, A.J.

History

Deposition	May 2, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 24, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bnr.cif.gz	221.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9bnr.ent.gz		Display	PDB format
PDBx/mmJSON format	9bnr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9bnr_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	9bnr_full_validation.pdf.gz	1.4 MB	Display
Data in XML	9bnr_validation.xml.gz	18.4 KB	Display
Data in CIF	9bnr_validation.cif.gz	25.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bn/9bnr ftp://data.pdbj.org/pub/pdb/validation_reports/bn/9bnr	HTTPS FTP

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Related structure data

Related structure data	9bnqC 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	#128 - Aug 2010 Interferons similarity (1) #94 - Oct 2007 Superoxide Dismutase similarity (1) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Macrophage migration inhibitory factor

B: Macrophage migration inhibitory factor

C: Macrophage migration inhibitory factor

hetero molecules

38.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	96.333, 96.333, 104.957
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Macrophage migration inhibitory factor / MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / ...MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / Phenylpyruvate tautomerase Mass: 12355.056 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MIF, GLIF, MMIF / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical	ChemComp-A1AQT / N-[2-(4-sulfamoylphenyl)ethyl]methanethioamide / 4-(2-isothiocyanatoethyl)benzenesulfonamide bound form Mass: 244.334 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₂N₂O₂S₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.79 Å³/Da / Density % sol: 67.57 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 uL 11 mg/mL MIF (100 mM Tris-HCl pH 8.0, 200 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 33 uL of 2.0 M Ammonium sulfate, 0.1 M HEPES pH 7.0, ...Details: 0.2 uL 11 mg/mL MIF (100 mM Tris-HCl pH 8.0, 200 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 33 uL of 2.0 M Ammonium sulfate, 0.1 M HEPES pH 7.0, 3% Isopropanol and <5mM 4-(2-isothiocyanatoethyl)benzenesulfonamide (10% DMSO final). Crystal was frozen in a solution of ~25% Glycerol, 75% reservoir

Crystal

Density Matthews: 3.79 Å³/Da / Density % sol: 67.57 %

Crystal grow

Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 uL 11 mg/mL MIF (100 mM Tris-HCl pH 8.0, 200 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 33 uL of 2.0 M Ammonium sulfate, 0.1 M HEPES pH 7.0, ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.954 Å / Relative weight: 1
Reflection	Resolution: 1.53→48.17 Å / Num. obs: 85163 / % possible obs: 99.8 % / Redundancy: 20 % / CC_1/2: 1 / R_merge(I) obs: 0.063 / R_pim(I) all: 0.015 / R_rim(I) all: 0.065 / Χ²: 1.04 / Net I/σ(I): 23.7 / Num. measured all: 1704479
Reflection shell	Resolution: 1.53→1.56 Å / % possible obs: 96.4 % / Redundancy: 17.6 % / R_merge(I) obs: 2.311 / Num. measured all: 70698 / Num. unique obs: 4020 / CC_1/2: 0.554 / R_pim(I) all: 0.552 / R_rim(I) all: 2.378 / Χ²: 1.03 / Net I/σ(I) obs: 1.4

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless	0.7.8	data scaling
XDS		data reduction
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.53→48.17 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1777	4312	5.07 %
R_work	0.1625	-	-
obs	0.1632	85072	99.78 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.53→48.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2601	0	90	201	2892

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2972
X-RAY DIFFRACTION	f_angle_d	1.092	4096
X-RAY DIFFRACTION	f_dihedral_angle_d	10.373	442
X-RAY DIFFRACTION	f_chiral_restr	0.074	442
X-RAY DIFFRACTION	f_plane_restr	0.02	545

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 (%)
1.53-1.55	0.2905	129	0.3132	2507	X-RAY DIFFRACTION	93
1.55-1.56	0.2753	162	0.2693	2661	X-RAY DIFFRACTION	100
1.56-1.58	0.2878	125	0.2402	2676	X-RAY DIFFRACTION	100
1.58-1.6	0.2305	154	0.237	2677	X-RAY DIFFRACTION	100
1.6-1.63	0.2417	138	0.2266	2623	X-RAY DIFFRACTION	100
1.63-1.65	0.2439	145	0.2197	2641	X-RAY DIFFRACTION	100
1.65-1.67	0.2601	139	0.2224	2715	X-RAY DIFFRACTION	100
1.67-1.7	0.2546	161	0.2224	2648	X-RAY DIFFRACTION	100
1.7-1.72	0.1973	158	0.2081	2683	X-RAY DIFFRACTION	100
1.72-1.75	0.2296	158	0.2061	2668	X-RAY DIFFRACTION	100
1.75-1.78	0.2513	131	0.1967	2691	X-RAY DIFFRACTION	100
1.78-1.81	0.2142	144	0.1872	2669	X-RAY DIFFRACTION	100
1.81-1.85	0.1821	150	0.1745	2678	X-RAY DIFFRACTION	100
1.85-1.89	0.1866	171	0.1604	2622	X-RAY DIFFRACTION	100
1.89-1.93	0.1663	122	0.1523	2727	X-RAY DIFFRACTION	100
1.93-1.97	0.181	123	0.1527	2707	X-RAY DIFFRACTION	100
1.97-2.02	0.1509	140	0.154	2654	X-RAY DIFFRACTION	100
2.02-2.08	0.1692	124	0.1565	2709	X-RAY DIFFRACTION	100
2.08-2.14	0.168	146	0.1554	2707	X-RAY DIFFRACTION	100
2.14-2.21	0.188	127	0.1607	2704	X-RAY DIFFRACTION	100
2.21-2.28	0.1907	145	0.1537	2702	X-RAY DIFFRACTION	100
2.28-2.38	0.1567	178	0.1483	2678	X-RAY DIFFRACTION	100
2.38-2.48	0.1914	161	0.1553	2676	X-RAY DIFFRACTION	100
2.48-2.61	0.1663	131	0.166	2726	X-RAY DIFFRACTION	100
2.61-2.78	0.1899	143	0.1616	2724	X-RAY DIFFRACTION	100
2.78-2.99	0.166	135	0.1603	2726	X-RAY DIFFRACTION	100
2.99-3.29	0.1728	138	0.1614	2737	X-RAY DIFFRACTION	100
3.29-3.77	0.1621	150	0.1468	2747	X-RAY DIFFRACTION	100
3.77-4.75	0.133	131	0.1387	2787	X-RAY DIFFRACTION	100
4.75-48.17	0.2014	153	0.1725	2890	X-RAY DIFFRACTION	100

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	3.4073	1.3984	-0.7643	7.1587	5.1869	5.8101	-0.1548	0.0411	-0.0259	-0.3556	0.2402	-0.3507	-0.159	0.1484	-0.0695	0.2486	-0.0077	-0.0233	0.1512	0.0353	0.1838	-34.5558	17.7776	-4.2144
2	7.1737	-5.1672	-5.9006	3.9339	4.5353	7.8399	-0.0981	0.4493	-0.0018	-0.0153	-0.0993	0.1013	-0.0859	-0.2866	0.1904	0.3774	-0.1244	0.0208	0.2528	-0.0299	0.2873	-36.1768	29.0373	1.9779
3	4.4951	-1.998	-1.5381	3.9559	4.8535	6.2788	0.1243	-0.3645	0.2281	0.0652	-0.1233	-0.1677	-0.229	-0.1624	0.0721	0.326	-0.0641	0.0014	0.2168	-0.0166	0.2133	-37.0102	24.3768	7.8955
4	7.0493	1.7222	5.3725	6.054	1.0207	6.3874	-0.0076	0.1883	-0.002	-0.3335	0.0151	-0.1063	-0.0266	0.2524	0.0185	0.2948	-0.0182	0.0521	0.1875	-0.0146	0.2123	-40.4469	10.522	-11.8613
5	6.0395	0.0808	-3.0543	0.6982	-1.8308	7.1033	0.0434	-0.2653	0.3283	0.1417	-0.01	0.1232	-0.0453	-0.0849	-0.082	0.2511	-0.038	-0.0135	0.1665	-0.0237	0.2109	-46.8582	21.6312	4.2511
6	5.0996	-4.7625	-4.8352	4.5535	4.5241	4.5962	0.2318	-0.089	0.3082	-0.4603	-0.1311	0.0754	-0.7288	0.1739	-0.1702	0.4418	-0.0525	-0.0427	0.2196	-0.0021	0.2538	-44.492	27.9929	-4.6474
7	1.4277	0.0179	0.4474	1.3721	1.8152	2.5756	0.0684	-0.0203	0.1163	-0.1453	-0.0748	0.1378	-0.1878	-0.2037	-0.0242	0.3155	-0.0106	-0.0432	0.1768	-0.0026	0.2422	-46.9667	19.7592	-1.4825
8	3.509	1.5401	3.3639	6.1395	-0.849	4.2136	0.1761	-0.5055	0.3623	0.525	-0.0685	0.2469	-0.1305	-0.0567	-0.0679	0.3777	-0.1034	-0.0148	0.3392	-0.033	0.2738	-41.155	19.0295	21.5847
9	6.0518	-3.2645	3.5248	3.0517	-0.8047	4.2703	0.121	0.0778	0.0585	-0.0103	0.0238	-0.2032	0.0856	0.2331	-0.1766	0.257	-0.0603	0.0095	0.1449	0.0188	0.2546	-41.1516	-0.1691	-5.4052
10	9.3169	-8.1363	-6.8096	8.7704	4.4149	6.8304	-0.0576	0.2394	-0.242	-0.0727	-0.1798	0.2923	0.0251	-0.2612	0.2396	0.2845	-0.0262	-0.0291	0.1519	-0.0078	0.1985	-51.7257	1.6768	-12.2568
11	8.2392	3.1864	0.3277	2.0208	1.4714	2.2927	-0.4737	0.9617	1.4514	-0.5379	0.2049	1.2167	-0.4782	-0.372	0.1342	0.3138	0.0249	-0.1091	0.2689	0.042	0.4365	-56.2508	10.6722	-13.8254
12	3.3694	-0.6838	1.5452	0.8826	-0.3094	3.2448	0.0518	-0.1186	-0.1423	0.2329	-0.0223	-0.1096	0.2493	0.0987	-0.0447	0.2944	-0.0281	-0.0239	0.1489	-0.0061	0.2333	-42.1693	0.1375	1.7898
13	6.8613	5.4273	-3.1451	5.5334	-0.7882	3.8816	-0.1865	0.2055	0.3168	0.0885	-0.1874	1.2657	-0.0436	-0.514	0.1534	0.2679	0.036	-0.0458	0.3082	-0.1048	0.4242	-61.266	9.715	-2.2961
14	9.0928	-3.2874	-3.0125	4.218	2.1292	2.3437	-0.0019	-0.0378	-0.1996	0.0633	-0.186	0.2887	0.1142	-0.1756	0.2296	0.3256	-0.0577	0.0085	0.2151	-0.0282	0.2785	-55.0155	-3.7578	-3.4769
15	4.3406	-2.4708	0.4829	2.6013	-0.6917	2.2499	0.0334	-0.1953	-0.0431	0.2277	-0.1151	-0.0594	0.2847	-0.2019	0.1029	0.3126	-0.0913	0.0019	0.1908	0.0065	0.2229	-49.7907	-2.8263	2.8265
16	6.8271	2.8753	-4.1855	4.0354	-4.3948	5.1076	0.1294	0.0787	0.2634	-0.4758	-0.1788	0.6605	-0.5452	-0.4394	-0.0074	0.3508	0.0355	-0.089	0.1815	-0.0538	0.3054	-54.3385	21.6323	-4.8004
17	6.3115	2.5986	-2.7981	3.8331	-2.222	6.381	0.0141	-0.0563	-0.514	0.1341	-0.0361	-0.4904	0.5799	0.5108	0.0067	0.3436	0.0211	-0.0874	0.2101	-0.0452	0.3072	-31.8398	4.8206	10.8874
18	4.8464	-2.1143	-5.7074	4.4185	2.0401	6.8692	-0.0713	-0.5278	-0.4182	0.962	-0.1005	-0.2801	0.8592	0.0831	0.2267	0.6301	-0.1075	-0.1413	0.3189	0.0641	0.2942	-38.4933	-1.0335	19.4031
19	4.3864	0.0615	-3.806	5.0932	-3.3869	5.8611	-0.0636	-0.3	-0.1596	0.5159	0.0505	0.3637	0.7068	-0.0976	-0.0264	0.5725	-0.1525	-0.0423	0.2468	0.043	0.2229	-43.7874	-2.3246	14.1264
20	5.3042	-2.8345	-1.0407	8.007	4.9047	8.2482	0.0082	-0.2398	0.0335	0.0077	0.2191	-0.6157	-0.0032	0.563	-0.2393	0.2136	-0.0621	0.0079	0.2718	-0.0086	0.287	-29.509	16.8722	7.8098
21	7.1158	1.9629	-0.0503	3.4173	1.2421	3.0432	0.2504	-0.4367	-0.1037	0.5573	-0.1019	0.015	0.3055	0.0841	-0.1394	0.3527	-0.0807	-0.034	0.2121	0.0113	0.1965	-39.8534	11.1211	18.7588
22	6.1571	-4.0169	-0.9325	6.696	4.7549	9.4109	0.0816	-0.3895	0.018	0.5819	-0.2634	0.4135	0.3612	-0.4346	0.1998	0.3408	-0.1398	0.0655	0.2533	-0.0354	0.274	-56.9496	-1.4294	7.6675

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 30 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 31 through 42 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 43 through 56 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 57 through 68 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 69 through 87 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 88 through 105 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 106 through 114 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 17 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 18 through 30 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 31 through 37 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 38 through 63 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 64 through 68 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 69 through 87 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 88 through 100 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 101 through 114 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1 through 17 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 18 through 30 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 31 through 42 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 43 through 56 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 57 through 100 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 101 through 114 )

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About Yorodumi

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Yorodumi