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- PDB-9bnq: N-(4-(isothiocyanatomethyl)phenyl)methanesulfonamide complexed wi... -

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Basic information

Entry
Database: PDB / ID: 9bnq
TitleN-(4-(isothiocyanatomethyl)phenyl)methanesulfonamide complexed with Macrophage Migration Inhibitory Factor
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / 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 / dopachrome isomerase activity / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate 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 / dopachrome isomerase activity / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonate 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 / negative regulation of protein metabolic process / prostaglandin biosynthetic 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 peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-serine phosphorylation / protease binding / secretory granule lumen / 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 / cytosol / cytoplasm
Similarity search - Function
Macrophage migration inhibitory factor, conserved site / Macrophage migration inhibitory factor family signature. / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
: / ISOPROPYL ALCOHOL / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsFellner, M. / Rutledge, M.T. / Putha, L. / Kok, L.K. / Gamble, A.B. / Wilbanks, S.M. / Vernall, A.J. / Tyndall, J.D.A.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: 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
DepositionMay 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage migration inhibitory factor
B: Macrophage migration inhibitory factor
C: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,39913
Polymers37,0653
Non-polymers1,33410
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-84 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.818, 67.818, 148.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#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-A1AQU / N-{[4-(methanesulfonamido)phenyl]methyl}methanethioamide / N-(4-(isothiocyanatomethyl)phenyl)methanesulfonamide 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.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
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 2.1 M Ammonium sulfate, 0.1 M Tris pH 7.5, ...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 2.1 M Ammonium sulfate, 0.1 M Tris pH 7.5, 3% Isopropanol and <5mM N-(4-(isothiocyanatomethyl)phenyl)methanesulfonamide (10% DMSO final). Crystal was frozen in a solution of ~25% Glycerol, 75% reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.09→47.95 Å / Num. obs: 143554 / % possible obs: 99.2 % / Redundancy: 23.2 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.014 / Rrim(I) all: 0.07 / Χ2: 1.04 / Net I/σ(I): 24.1 / Num. measured all: 3336440
Reflection shellResolution: 1.09→1.11 Å / % possible obs: 88.1 % / Redundancy: 8 % / Rmerge(I) obs: 1.665 / Num. measured all: 49205 / Num. unique obs: 6189 / CC1/2: 0.411 / Rpim(I) all: 0.613 / Rrim(I) all: 1.782 / Χ2: 1.07 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.8data scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→39.9 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 13.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1537 7259 5.06 %
Rwork0.1366 --
obs0.1375 143349 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.09→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 78 242 2921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093031
X-RAY DIFFRACTIONf_angle_d1.0014180
X-RAY DIFFRACTIONf_dihedral_angle_d9.855459
X-RAY DIFFRACTIONf_chiral_restr0.089448
X-RAY DIFFRACTIONf_plane_restr0.016558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.10.36952200.37673795X-RAY DIFFRACTION84
1.1-1.110.30832090.2694154X-RAY DIFFRACTION92
1.11-1.130.24922170.2284383X-RAY DIFFRACTION97
1.13-1.140.21132320.19514466X-RAY DIFFRACTION99
1.14-1.160.1642150.15984545X-RAY DIFFRACTION100
1.16-1.170.15862340.13824531X-RAY DIFFRACTION100
1.17-1.190.15712550.12864512X-RAY DIFFRACTION100
1.19-1.210.15742320.12764527X-RAY DIFFRACTION100
1.21-1.230.16832250.1264539X-RAY DIFFRACTION100
1.23-1.250.13692650.12934518X-RAY DIFFRACTION100
1.25-1.270.14482210.12724538X-RAY DIFFRACTION100
1.27-1.290.15012300.12424540X-RAY DIFFRACTION100
1.29-1.310.12672310.11184582X-RAY DIFFRACTION100
1.31-1.340.11982450.1094513X-RAY DIFFRACTION100
1.34-1.370.12812530.11184540X-RAY DIFFRACTION100
1.37-1.40.13262530.10974546X-RAY DIFFRACTION100
1.4-1.440.13412790.11014533X-RAY DIFFRACTION100
1.44-1.480.13072270.11184566X-RAY DIFFRACTION100
1.48-1.520.12232270.11294584X-RAY DIFFRACTION100
1.52-1.570.13592330.11344578X-RAY DIFFRACTION100
1.57-1.630.13972420.11714580X-RAY DIFFRACTION100
1.63-1.690.1442420.1214573X-RAY DIFFRACTION100
1.69-1.770.14112460.12244593X-RAY DIFFRACTION100
1.77-1.860.14732640.12424582X-RAY DIFFRACTION100
1.86-1.980.12792650.11764593X-RAY DIFFRACTION100
1.98-2.130.13732600.12154627X-RAY DIFFRACTION100
2.13-2.340.13852390.12154672X-RAY DIFFRACTION100
2.34-2.680.152330.13894698X-RAY DIFFRACTION100
2.68-3.380.15812950.14254698X-RAY DIFFRACTION100
3.38-39.90.17872700.16224984X-RAY DIFFRACTION100

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