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- PDB-1qbn: Bovine Trypsin 2-[amino(imino)methyl]-2-hydroxyphenoxy]-6-[3-(4,5... -

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Basic information

Entry
Database: PDB / ID: 1qbn
TitleBovine Trypsin 2-[amino(imino)methyl]-2-hydroxyphenoxy]-6-[3-(4,5-dihydro-1H-imidazol-2-yl)phenoxy]pyridine-4-carboxylic Acid (ZK-806688) Complex
ComponentsPROTEIN (TRYPSIN)
KeywordsHYDROLASE / SERINE PROTEINASE / PROTEIN-INHIBITOR COMPLEX / S1 POCKET
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-688 / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / DIRECT REPLACEMENT / Resolution: 1.8 Å
AuthorsWhitlow, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallographic analysis of potent and selective factor Xa inhibitors complexed to bovine trypsin.
Authors: Whitlow, M. / Arnaiz, D.O. / Buckman, B.O. / Davey, D.D. / Griedel, B. / Guilford, W.J. / Koovakkat, S.K. / Liang, A. / Mohan, R. / Phillips, G.B. / Seto, M. / Shaw, K.J. / Xu, W. / Zhao, Z. ...Authors: Whitlow, M. / Arnaiz, D.O. / Buckman, B.O. / Davey, D.D. / Griedel, B. / Guilford, W.J. / Koovakkat, S.K. / Liang, A. / Mohan, R. / Phillips, G.B. / Seto, M. / Shaw, K.J. / Xu, W. / Zhao, Z. / Light, D.R. / Morrissey, M.M.
#1: Journal: FEBS Lett. / Year: 1978
Title: Crystal Structure Analysis and Refinement of Two Variants of Trigonal Trypsinogen
Authors: Bode, W. / Huber, R.
#2: Journal: J.Med.Chem. / Year: 1999
Title: Design, Synthesis, and Activity of 2,6-Diphenoxypyridine-Derived Factor Xa Inhibitors
Authors: Phillips, G. / Davey, D. / Eagen, K. / Ng, H.P. / Pinkerton, M. / Koovakkat, S.K. / Whitlow, M. / Liang, A. / Trinh, L. / Morrissey, M.M.
#3: Journal: J.Med.Chem. / Year: 1998
Title: Discovery of N-[2-[5-[Amino(imino)methyl]-2-hydroxyphenoxy]-3,5-difluoro-6-[3-(4,5-dihydro-1-methyl-1H-imidazol-2-yl)phenoxy] pyridin-4-yl-N-methylglycine (ZK-807834): A Potent, Selective and ...Title: Discovery of N-[2-[5-[Amino(imino)methyl]-2-hydroxyphenoxy]-3,5-difluoro-6-[3-(4,5-dihydro-1-methyl-1H-imidazol-2-yl)phenoxy] pyridin-4-yl-N-methylglycine (ZK-807834): A Potent, Selective and Orally Active Inhibitor of the Blood Coagulation Enzyme Factor Xa
Authors: Phillips, G.B. / Buckman, B.O. / Davey, D.D. / Eagen, K.A. / Guilford, W.J. / Hinchman, J. / Ho, E. / Koovakkat, S. / Liang, A. / Light, D.R. / Mohan, R. / Ng, H.P. / Post, J. / Smith, D. / ...Authors: Phillips, G.B. / Buckman, B.O. / Davey, D.D. / Eagen, K.A. / Guilford, W.J. / Hinchman, J. / Ho, E. / Koovakkat, S. / Liang, A. / Light, D.R. / Mohan, R. / Ng, H.P. / Post, J. / Smith, D. / Subramanyam, B. / Sullivan, M.E. / Trinh, L. / Vergona, R. / Walters, J. / White, K. / Whitlow, M. / Wu, S. / Xu, W. / Morrissey, M.M.
#4: Journal: FEBS Lett. / Year: 1995
Title: Crystal structures of factor Xa specific inhibitors in complex with trypsin: structural grounds for inhibition of factor Xa and selectivity against thrombin
Authors: Stubbs, M.T. / Huber, R. / Bode, W.
#5: Journal: Methods (San Diego) / Year: 1990
Title: Analytical and Production Seeding Techniques
Authors: Stura, E.A. / Wilson, I.A.
#6: Journal: J.Biol.Chem. / Year: 1996
Title: X-ray structure of Active Site-inhibited Clotting Factor Xa
Authors: Brandstetter, H. / Kuhne, A. / Bode, W. / Huber, R. / von der Saal, W. / Wirthensohn, K. / Engh, R.A.
History
DepositionApr 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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: PROTEIN (TRYPSIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8364
Polymers23,3241
Non-polymers5123
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.020, 55.020, 109.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
DetailsThe biological assembly is a monomer.

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Components

#1: Protein PROTEIN (TRYPSIN)


Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: BOVINE TRYPSIN / Source method: isolated from a natural source / Details: BOEHRINGER MANNHEIM CATALOG NUMBER 109,827 / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-688 / 2-[AMINO(IMINO)METHYL]-2-HYDROXYPHENOXY]-6-[3-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)PHENOXY]PYRIDINE-4-CARBOXYLIC ACID / ZK-806688


Mass: 431.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H17N5O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 39.82 %
Description: STARTING FROM THE TRYPSIN 2-AMINOBENZIMIDAZOLE STRUCTURE
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: MICROCRYSTALS GROWN USING THE HANGING DROP METHOD IN LINBRO CULTURE PLATES. CRYSTALLIZATION RESERVOIRS CONTAIN 1.8 - 2.0 M AMMONIUM SULFATE, 50 MM TRIS HCL, 10 MM CACL2, PH 7.4. SIX UL OF 15 ...Details: MICROCRYSTALS GROWN USING THE HANGING DROP METHOD IN LINBRO CULTURE PLATES. CRYSTALLIZATION RESERVOIRS CONTAIN 1.8 - 2.0 M AMMONIUM SULFATE, 50 MM TRIS HCL, 10 MM CACL2, PH 7.4. SIX UL OF 15 MG/ML BOVINE TRYPSIN IN 20 MM 2-AMINOBENZIMIDAZOLE WAS ADDED TO 6 UL OF RESERVOIR. MACROSEEDING WAS USED TO GROW LARGE CRYSTALS (REF 5). SINGLE CRYSTALS WERE WASHED IN 0.8 M AMMONIUM SULFATE, 50 MM TRIS HCL, 10 MM CACL2, PH 7.4. THE WASHED CRYSTALS WERE PLACED IN A 18 HOUR OLD HANGING, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.8-2.0 Mammonium sulfate1reservoir
250 mMTris-HCl1reservoir
310 mM1reservoirCaCl2
415 mg/mltrypsin1drop
520 mM2-aminobenzimidazole1drop

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 15, 1994 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. all: 16885 / Num. obs: 16575 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rsym value: 0.075 / Net I/σ(I): 9.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.36 / Rsym value: 0.226 / % possible all: 90
Reflection
*PLUS
Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 90 % / Rmerge(I) obs: 0.226

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PROFFTrefinement
RefinementMethod to determine structure: DIRECT REPLACEMENT / Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: Hendrickson, W.A. (1985): Methods in Enzymology 115, pp. 252-270
RfactorNum. reflection% reflection
Rfree0.217 693 4 %
Rwork0.155 --
all-16885 -
obs-16575 95.2 %
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 34 165 1836
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.030.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4972
X-RAY DIFFRACTIONp_mcangle_it2.1373
X-RAY DIFFRACTIONp_scbond_it2.9853
X-RAY DIFFRACTIONp_scangle_it4.1974
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1610.15
X-RAY DIFFRACTIONp_singtor_nbd0.1670.5
X-RAY DIFFRACTIONp_multtor_nbd0.1690.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2190.5
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor1715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor18.320
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 4 % / Rfactor obs: 0.154 / Rfactor Rwork: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it3
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it4

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