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- PDB-3wv1: Crystal structure of the catalytic domain of MMP-13 complexed wit... -

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Basic information

Entry
Database: PDB / ID: 3wv1
TitleCrystal structure of the catalytic domain of MMP-13 complexed with 4-(2-((6-fluoro-2-((3-methoxybenzyl)carbamoyl)-4-oxo-3,4-dihydroquinazolin-5-yl)oxy)ethyl)benzoic acid
ComponentsCollagenase 3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / MMP-13 / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation ...growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin ...Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Chem-WHH / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsOki, H. / Tanaka, Y.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Discovery of novel, highly potent, and selective quinazoline-2-carboxamide-based matrix metalloproteinase (MMP)-13 inhibitors without a zinc binding group using a structure-based design approach
Authors: Nara, H. / Sato, K. / Naito, T. / Mototani, H. / Oki, H. / Yamamoto, Y. / Kuno, H. / Santou, T. / Kanzaki, N. / Terauchi, J. / Uchikawa, O. / Kori, M.
History
DepositionMay 12, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagenase 3
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,01416
Polymers38,4712
Non-polymers1,54314
Water4,432246
1
A: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0078
Polymers19,2351
Non-polymers7717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0078
Polymers19,2351
Non-polymers7717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-16 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.372, 36.058, 95.298
Angle α, β, γ (deg.)90.000, 130.895, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Collagenase 3 / / Matrix metalloproteinase-13 / MMP-13


Mass: 19235.383 Da / Num. of mol.: 2 / Fragment: catalytic domain, residues 104-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 6 types, 260 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-WHH / 4-[2-({6-fluoro-2-[(3-methoxybenzyl)carbamoyl]-4-oxo-3,4-dihydroquinazolin-5-yl}oxy)ethyl]benzoic acid


Mass: 491.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H22FN3O6
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.27 Å3/Da / Density % sol: 45.77 % / Mosaicity: 0.665 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8-16%(w/v) PEG8000, 1.0-1.5M ammonium formate, 0.1M Tris HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→29.65 Å / Num. obs: 24131 / % possible obs: 98 % / Redundancy: 3.69 % / Rmerge(I) obs: 0.085 / Χ2: 0.99 / Net I/σ(I): 9.3 / Scaling rejects: 900
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.98-2.053.210.3213.3635919751.042380.5
2.05-2.133.780.33.5922824281.0142100
2.13-2.233.770.2714916624161.0660100
2.23-2.343.770.2294.6928024401.0472100
2.34-2.493.790.1885.5938324611.0150100
2.49-2.683.780.1526.5931724460.9866100
2.68-2.953.780.1089933224390.98101100
2.95-3.383.750.07411.9940224770.92106100
3.38-4.263.690.04918.8931424770.91177100
4.26-29.653.470.0424.4913625721.0220399.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata reduction
REFMAC5.2.0019refinement
PDB_EXTRACT3.14data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→29.65 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2038 / WRfactor Rwork: 0.1669 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8615 / SU B: 8.137 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1879 / SU Rfree: 0.1603 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1220 5.1 %RANDOM
Rwork0.1747 ---
obs0.177 24131 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.7 Å2 / Biso mean: 27.5761 Å2 / Biso min: 7.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å2-0.01 Å2
2---0.14 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.98→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 88 246 2990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212833
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9673849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1765331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2924.091132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65715405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.093155
X-RAY DIFFRACTIONr_chiral_restr0.0810.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022357
X-RAY DIFFRACTIONr_nbd_refined0.1980.21387
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21929
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2228
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.226
X-RAY DIFFRACTIONr_mcbond_it1.55721663
X-RAY DIFFRACTIONr_mcangle_it2.57532669
X-RAY DIFFRACTIONr_scbond_it3.74641262
X-RAY DIFFRACTIONr_scangle_it5.27261180
LS refinement shellResolution: 1.977→2.029 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 72 -
Rwork0.218 1256 -
all-1328 -
obs--73.49 %
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)
10.799-0.2057-0.87160.3872-0.00961.61050.00710.0382-0.00720.0694-0.04170.0043-0.01240.02120.0347-0.0039-0.00450.0032-0.0444-0.0017-0.024541.424-14.17-15.723
20.2014-0.06270.21520.67020.50650.73550.0659-0.0164-0.03050.1854-0.14770.05890.1276-0.03620.08180.0205-0.0770.0380.02280.0288-0.046710.674-22.469-26.133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A104 - 273
2X-RAY DIFFRACTION1A301 - 307
3X-RAY DIFFRACTION2B104 - 269
4X-RAY DIFFRACTION2B301 - 307

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