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- PDB-3mqe: Structure of SC-75416 bound at the COX-2 active site -

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Basic information

Entry
Database: PDB / ID: 3mqe
TitleStructure of SC-75416 bound at the COX-2 active site
ComponentsProstaglandin G/H synthase 2Cyclooxygenase
KeywordsOXIDOREDUCTASE / COX2 / COX-2 / PGH2S-2 / CYCLOOXYGENASE-2 / DIOXYGENASE / DISULFIDE BOND / ENDOPLASMIC RETICULUM / FATTY ACID BIOSYNTHESIS / GLYCOPROTEIN / HEME / IRON / LIPID SYNTHESIS / MEMBRANE / METAL-BINDING / MICROSOME / PEROXIDASE / PHOSPHOPROTEIN / PROSTAGLANDIN BIOSYNTHESIS
Function / homology
Function and homology information


Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / positive regulation of platelet-derived growth factor production / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / hair cycle / Nicotinamide salvaging ...Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / positive regulation of platelet-derived growth factor production / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / hair cycle / Nicotinamide salvaging / positive regulation of fibroblast growth factor production / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / negative regulation of synaptic transmission, dopaminergic / cellular response to lead ion / response to nematode / positive regulation of transforming growth factor beta production / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of prostaglandin biosynthetic process / regulation of neuroinflammatory response / positive regulation of synaptic plasticity / response to fatty acid / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / response to fructose / positive regulation of smooth muscle contraction / cyclooxygenase pathway / positive regulation of fever generation / response to vitamin D / prostaglandin secretion / cellular response to fluid shear stress / nuclear outer membrane / response to angiotensin / response to manganese ion / nuclear inner membrane / prostaglandin biosynthetic process / negative regulation of smooth muscle contraction / cellular response to ATP / maintenance of blood-brain barrier / positive regulation of cell migration involved in sprouting angiogenesis / bone mineralization / negative regulation of calcium ion transport / decidualization / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / response to tumor necrosis factor / brown fat cell differentiation / response to glucocorticoid / keratinocyte differentiation / positive regulation of vasoconstriction / embryo implantation / positive regulation of brown fat cell differentiation / positive regulation of synaptic transmission, glutamatergic / learning / response to cytokine / caveola / peroxidase activity / positive regulation of smooth muscle cell proliferation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / memory / regulation of blood pressure / positive regulation of protein import into nucleus / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / response to estradiol / positive regulation of peptidyl-serine phosphorylation / cellular response to heat / regulation of cell population proliferation / cellular response to hypoxia / angiogenesis / response to oxidative stress / response to lipopolysaccharide / neuron projection / response to xenobiotic stimulus / positive regulation of apoptotic process / negative regulation of cell population proliferation / positive regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / metal ion binding / cytoplasm
Similarity search - Function
Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily ...Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Chem-416 / PROTOPORPHYRIN IX CONTAINING FE / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, J.L. / Limburg, D. / Graneto, M.J. / Springer, J. / Rogier, J. / Kiefer, J.R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: The novel benzopyran class of selective cyclooxygenase-2 inhibitors. Part 2: The second clinical candidate having a shorter and favorable human half-life.
Authors: Wang, J.L. / Limburg, D. / Graneto, M.J. / Springer, J. / Hamper, J.R. / Liao, S. / Pawlitz, J.L. / Kurumbail, R.G. / Maziasz, T. / Talley, J.J. / Kiefer, J.R. / Carter, J.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,00026
Polymers269,3314
Non-polymers8,67022
Water1,74797
1
A: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,00013
Polymers134,6652
Non-polymers4,33511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-15 kcal/mol
Surface area44930 Å2
MethodPISA
2
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,00013
Polymers134,6652
Non-polymers4,33511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-17 kcal/mol
Surface area44880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.701, 140.378, 129.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A55 - 500
2114B55 - 500
3114C55 - 500
4114D55 - 500

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Prostaglandin G/H synthase 2 / Cyclooxygenase / Cyclooxygenase-2 / COX-2 / Prostaglandin-endoperoxide synthase 2 / Prostaglandin H2 synthase 2 / ...Cyclooxygenase-2 / COX-2 / Prostaglandin-endoperoxide synthase 2 / Prostaglandin H2 synthase 2 / PGH synthase 2 / PGHS-2 / PHS II / Glucocorticoid-regulated inflammatory cyclooxygenase / Gripghs / TIS10 protein / Macrophage activation-associated marker protein P71/73 / PES-2


Mass: 67332.711 Da / Num. of mol.: 4 / Fragment: mCOX-2 c delta (UNP residues 18 to 604)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cox-2, Cox2, Pghs-b, Ptgs2, Tis10 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q05769, prostaglandin-endoperoxide synthase

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Sugars , 3 types, 14 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 105 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical
ChemComp-416 / (2S)-7-tert-butyl-6-chloro-2-(trifluoromethyl)-2H-chromene-3-carboxylic acid


Mass: 334.718 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H14ClF3O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 60.39 %
Crystal growTemperature: 291 K / Details: VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2000 / Details: CRYSTAL MONOCHROMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 82436 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.112 / Net I/σ(I): 9.4
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.43 / Rsym value: 0.447 / % possible all: 99

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 40.628 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R Free: 0.422 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29028 8264 10.1 %RANDOM
Rwork0.23575 ---
obs0.24126 73941 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.496 Å2
Baniso -1Baniso -2Baniso -3
1--4.72 Å20 Å20 Å2
2--6.86 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17896 0 580 97 18573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02218970
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212968
X-RAY DIFFRACTIONr_angle_refined_deg1.272.00425810
X-RAY DIFFRACTIONr_angle_other_deg0.911331484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7952204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80724.107896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.075153104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0881592
X-RAY DIFFRACTIONr_chiral_restr0.0680.22742
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02120744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023856
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2291.511036
X-RAY DIFFRACTIONr_mcbond_other0.0491.54416
X-RAY DIFFRACTIONr_mcangle_it0.44217936
X-RAY DIFFRACTIONr_scbond_it0.74837934
X-RAY DIFFRACTIONr_scangle_it1.2644.57874
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6295 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.260.5
2Bmedium positional0.250.5
3Cmedium positional0.240.5
4Dmedium positional0.260.5
1Amedium thermal0.232
2Bmedium thermal0.242
3Cmedium thermal0.212
4Dmedium thermal0.22
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 587 -
Rwork0.356 5313 -
obs--98.94 %
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)
11.69460.0176-0.08670.5403-0.3020.96060.05570.01320.10740.021-0.02630.0547-0.0201-0.1955-0.02940.13850.00510.00390.0318-0.01360.137421.9817-23.4941-64.2333
21.4191-0.00330.13070.5934-0.46580.82640.0674-0.04060.1223-0.0058-0.0745-0.0871-0.00820.14170.00710.15930.00060.00890.0134-0.01960.141660.6864-29.591-55.282
31.46660.09850.10320.43050.26461.0977-0.0355-0.0709-0.14540.04790.0261-0.06630.10850.2040.00930.17730.03130.02310.09670.02680.166673.6882-46.83060.6808
41.24090.0464-0.07380.7050.41370.9354-0.03310.0397-0.09850.0172-0.01540.09510.0647-0.14860.04860.1552-0.00850.02410.13180.02080.14235.0139-40.57529.5842
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 681
2X-RAY DIFFRACTION2B18 - 681
3X-RAY DIFFRACTION3C18 - 681
4X-RAY DIFFRACTION4D18 - 681

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