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- PDB-4crb: Creating novel F1 inhibitors through fragment based lead generati... -

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Entry
Database: PDB / ID: 4crb
TitleCreating novel F1 inhibitors through fragment based lead generation and structure aided drug design
ComponentsCOAGULATION FACTOR XIFactor XI
KeywordsHYDROLASE
Function / homology
Function and homology information


Intrinsic Pathway of Fibrin Clot Formation / ec:3.4.21.27: / serine-type aminopeptidase activity / positive regulation of fibrinolysis / plasminogen activation / blood coagulation, intrinsic pathway / heparin binding / blood coagulation / serine-type endopeptidase activity / extracellular space ...Intrinsic Pathway of Fibrin Clot Formation / ec:3.4.21.27: / serine-type aminopeptidase activity / positive regulation of fibrinolysis / plasminogen activation / blood coagulation, intrinsic pathway / heparin binding / blood coagulation / serine-type endopeptidase activity / extracellular space / extracellular exosome / membrane / extracellular region / identical protein binding / plasma membrane
Serine proteases, trypsin domain / Peptidase S1A, chymotrypsin family / PAN/Apple domain profile. / Serine proteases, trypsin domain profile. / Apple domain. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin family, histidine active site. / Trypsin / PAN domain / Serine proteases, trypsin family, serine active site ...Serine proteases, trypsin domain / Peptidase S1A, chymotrypsin family / PAN/Apple domain profile. / Serine proteases, trypsin domain profile. / Apple domain. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin family, histidine active site. / Trypsin / PAN domain / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site / Peptidase S1, PA clan / PAN/Apple domain / Apple domain
Coagulation factor XI
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSandmark, J. / Oster, L. / Fjellstrom, O. / Akkaya, S. / Beisel, H.G. / Eriksson, P.O. / Erixon, K. / Gustafsson, D. / Jurva, U. / Kang, D. / Karis, D. / Knecht, W. / Nerme, V. / Nilsson, I. / Olsson, T. / Redzic, A. / Roth, R. / Tigerstrom, A.
CitationJournal: Plos One / Year: 2015
Title: Creating Novel Activated Factor Xi Inhibitors Through Fragment Based Lead Generation and Structure Aided Drug Design.
Authors: Fjellstrom, O. / Akkaya, S. / Beisel, H. / Eriksson, P. / Erixon, K. / Gustafsson, D. / Jurva, U. / Kang, D. / Karis, D. / Knecht, W. / Nerme, V. / Nilsson, I. / Olsson, T. / Redzic, A. / Roth, R. / Sandmark, J. / Tigerstrom, A. / Oster, L.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 26, 2014 / Release: Feb 11, 2015
RevisionDateData content typeProviderType
1.0Feb 11, 2015Structure modelrepositoryInitial release
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAGULATION FACTOR XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8798
Polymers26,7521
Non-polymers1,1267
Water2,198122
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)120.990, 120.990, 120.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-1488-

SO4

21A-1488-

SO4

31A-2122-

HOH

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Components

#1: Protein/peptide COAGULATION FACTOR XI / Factor XI / FXI / PLASMA THROMBOPLASTIN ANTECEDENT / PTA / COAGULATION FACTOR XIA LIGHT CHAIN


Mass: 26752.369 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 388-625 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P03951, EC: 3.4.21.27
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Glycerol
#3: Chemical ChemComp-7P0 / N-[(1S)-1-benzyl-2-[2-[5-chloro-2-(tetrazol-1-yl)phenyl]ethylamino]-2-oxo-ethyl]-4-hydroxy-2-oxo-1H-quinoline-6-carboxamide


Mass: 557.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24ClN7O4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 55.41 % / Description: NONE
Crystal growpH: 8.5 / Details: 2M AMMONIUM SULFATE 0.1M TRIS-CL PH 8.5 0.2M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 25023 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.85→42.7 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1267 5.2 %RANDOM
Rwork0.19 ---
Obs0.191 23299 97.7 %-
Refinement stepCycle: LAST / Resolution: 1.85→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 72 122 2075

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