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- PDB-4axm: TRIAZINE CATHEPSIN INHIBITOR COMPLEX -

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Basic information

Entry
Database: PDB / ID: 4axm
TitleTRIAZINE CATHEPSIN INHIBITOR COMPLEX
ComponentsCATHEPSIN L1
KeywordsHYDROLASE
Function / homology
Function and homology information


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / Collagen degradation / fibronectin binding / antigen processing and presentation / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / Attachment and Entry / positive regulation of apoptotic signaling pathway / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / proteolysis involved in protein catabolic process / lysosomal lumen / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / adaptive immune response / lysosome / immune response / symbiont entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-V65 / Procathepsin L
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEhmke, V. / Diederich, F. / Banner, D.W. / Benz, J.
CitationJournal: Chemmedchem / Year: 2013
Title: Optimization of Triazine Nitriles as Rhodesain Inhibitors: Structure-Activity Relationships, Bioisosteric Imidazopyridine Nitriles, and X-Ray Crystal Structure Analysis with Human Cathepsin L
Authors: Ehmke, V. / Winkler, E. / Banner, D.W. / Haap, W. / Schweizer, W.B. / Rottmann, M. / Kaiser, M. / Freymond, C. / Schirmeister, T. / Diederich, F.
History
DepositionJun 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_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: CATHEPSIN L1
B: CATHEPSIN L1
F: CATHEPSIN L1
I: CATHEPSIN L1
L: CATHEPSIN L1
O: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,28818
Polymers145,1506
Non-polymers3,13812
Water3,873215
1
A: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7153
Polymers24,1921
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7153
Polymers24,1921
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
F: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7153
Polymers24,1921
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
I: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7153
Polymers24,1921
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
L: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7153
Polymers24,1921
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
O: CATHEPSIN L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7153
Polymers24,1921
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.842, 134.781, 140.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CATHEPSIN L1 / / CATHEPSIN L / MAJOR EXCRETED PROTEIN / MEP / CATHEPSIN L1 HEAVY CHAIN / CATHEPSIN L1 LIGHT CHAIN


Mass: 24191.701 Da / Num. of mol.: 6 / Fragment: CATALYTIC, RESIDUES 114-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07711, cathepsin L
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-V65 / 4-[(4-chlorobenzyl)(cyclohexyl)amino]-6-morpholin-4-yl-1,3,5-triazine-2-carboxamide


Mass: 430.931 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27ClN6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.76 Å3/Da / Density % sol: 55.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.72→48.7 Å / Num. obs: 44662 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.72 % / Biso Wilson estimate: 55.9 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 7.34
Reflection shellResolution: 2.72→2.82 Å / Redundancy: 7.01 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.32 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0025refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YJC

2yjc


Resolution: 2.8→46.97 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.889 / SU B: 34.469 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS COMPUTED AT RIDING POSITIONS BY REFMAC BUT NOT OUTPUT. THERE ARE 6 INDEPENDENT COMPLEXES WITH VARYING LIGAND OCCUPANCIES. NCS WAS NOT USED
RfactorNum. reflection% reflectionSelection details
Rfree0.25716 1949 5 %RANDOM
Rwork0.18777 ---
obs0.19124 37373 95.83 %-
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: 57.296 Å2
Baniso -1Baniso -2Baniso -3
1-6.51 Å20 Å20 Å2
2---2.11 Å20 Å2
3----4.39 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10043 0 210 215 10468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910943
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.96114835
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98151368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55725.135518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48151721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5141536
X-RAY DIFFRACTIONr_chiral_restr0.0960.21448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218660
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 117 -
Rwork0.349 2572 -
obs--89.9 %
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)
10.8942-0.7147-0.68121.6330.77431.53980.0377-0.03840.0162-0.0265-0.0230.04470.0086-0.0304-0.01480.0530.022-0.01330.06530.01110.1267-17.55617.263-36.056
21.87330.58120.93941.77250.51242.24830.05220.1049-0.0329-0.01310.05390.07320.05750.3239-0.10620.03260.0275-0.0470.0796-0.01520.1137-20.78949.948-70.446
30.93540.4267-0.19481.58690.99591.73070.09120.0362-0.0180.11680.03280.02030.12180.0018-0.12410.04170.0045-0.02380.06420.02250.1131-14.68463.167-32.827
41.88011.34881.11422.90120.59442.2706-0.1851-0.0020.0598-0.31480.00320.093-0.078-0.13480.18190.06740.0294-0.0430.0555-0.01850.0995-20.2124.133-73.708
52.15430.7466-1.14583.1506-2.50993.5892-0.0720.08140.1021-0.13190.0841-0.03920.0265-0.2919-0.0120.0838-0.0183-0.0140.0754-0.00040.0126-18.61840.592-1.499
62.42160.93150.10762.9877-0.30142.62990.06590.09980.0679-0.1419-0.0138-0.07260.0611-0.0073-0.05210.08550.03030.00770.02360.01470.015917.61339.433-35.545
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 220
2X-RAY DIFFRACTION2B1 - 220
3X-RAY DIFFRACTION3F1 - 220
4X-RAY DIFFRACTION4I1 - 220
5X-RAY DIFFRACTION5L1 - 220
6X-RAY DIFFRACTION6O1 - 220

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