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- PDB-4cdf: Human DPP1 in complex with (2S,4S)-N-((1S)-1-cyano-2-(4-(4- cyano... -

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Basic information

Entry
Database: PDB / ID: 4cdf
TitleHuman DPP1 in complex with (2S,4S)-N-((1S)-1-cyano-2-(4-(4- cyanophenyl)phenyl)ethyl)-4-hydroxy-piperidine-2-carboxamide
Components(DIPEPTIDYL PEPTIDASE 1 ...) x 3
KeywordsHYDROLASE / INHIBITOR
Function / homology
Function and homology information


dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / phosphatase binding / endoplasmic reticulum-Golgi intermediate compartment membrane / MHC class II antigen presentation / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / T cell mediated cytotoxicity / azurophil granule lumen / protein-folding chaperone binding / : / lysosome / immune response / endoplasmic reticulum lumen / serine-type endopeptidase activity / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane
Similarity search - Function
Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. ...Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / 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 / Lipocalin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-W2C / Dipeptidyl peptidase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDebreczeni, J. / Edman, K. / Furber, M. / Tiden, A. / Gardiner, P. / Mete, T. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. ...Debreczeni, J. / Edman, K. / Furber, M. / Tiden, A. / Gardiner, P. / Mete, T. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. / Kinchin, E. / Luckhurst, C. / Cage, P. / Sanghanee, H. / Breed, J. / Wissler, L.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Cathepsin C Inhibitors: Property Optimization and Identification of a Clinical Candidate.
Authors: Furber, M. / Gardiner, P. / Tiden, A.K. / Mete, A. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. / Kinchin, E. / Luckhurst, C. / Barber, S. / Cage, P. / Sanganee, H. / Austin, R. / ...Authors: Furber, M. / Gardiner, P. / Tiden, A.K. / Mete, A. / Ford, R. / Millichip, I. / Stein, L. / Mather, A. / Kinchin, E. / Luckhurst, C. / Barber, S. / Cage, P. / Sanganee, H. / Austin, R. / Chohan, K. / Beri, R. / Thong, B. / Wallace, A. / Oreffo, V. / Hutchinson, R. / Harper, S. / Debreczeni, J. / Breed, J. / Wissler, L. / Edman, K.
History
DepositionOct 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
B: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
C: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
D: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
E: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
F: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,56414
Polymers79,8566
Non-polymers1,7098
Water2,072115
1
A: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
B: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
C: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7827
Polymers39,9283
Non-polymers8544
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-63.4 kcal/mol
Surface area16030 Å2
MethodPISA
2
D: DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
E: DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
F: DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7827
Polymers39,9283
Non-polymers8544
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-62.6 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.850, 84.850, 222.452
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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DIPEPTIDYL PEPTIDASE 1 ... , 3 types, 6 molecules ADBECF

#1: Protein DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN / DIPEPTIDYL PEPTIDASE I EXCLUSION DOMAIN CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I ...DIPEPTIDYL PEPTIDASE I EXCLUSION DOMAIN CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / DPPI / DIPEPTIDYL TRANSFERASE


Mass: 13601.268 Da / Num. of mol.: 2 / Fragment: DPP1 EXCLUSION DOMAIN, RESIDUES 25-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I
#2: Protein DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN / DIPEPTIDYL PEPTIDASE I HEAVY CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / ...DIPEPTIDYL PEPTIDASE I HEAVY CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / DPPI / DIPEPTIDYL TRANSFERASE


Mass: 18743.174 Da / Num. of mol.: 2 / Fragment: DPP1 HEAVY CHAIN, RESIDUES 229-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I
#3: Protein DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN / DIPEPTIDYL PEPTIDASE I LIGHT CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / ...DIPEPTIDYL PEPTIDASE I LIGHT CHAIN / CATHEPSIN C / CATHEPSIN J / DIPEPTIDYL PEPTIDASE I / DPP-I / DPPI / DIPEPTIDYL TRANSFERASE


Mass: 7583.444 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I

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Sugars , 1 types, 4 molecules

#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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

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Non-polymers , 3 types, 119 molecules

#5: Chemical ChemComp-W2C / (2S,4S)-N-[(2S)-1-azanylidene-3-[4-(4-cyanophenyl)phenyl]propan-2-yl]-4-oxidanyl-piperidine-2-carboxamide


Mass: 376.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24N4O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): POSTTRANSLATIONAL MODIFICATION

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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: 2.89 Å3/Da / Density % sol: 75.51 % / Description: NONE
Crystal growDetails: 21% PEG3350, 200MM AMSO4, 100MM NA ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→44.34 Å / Num. obs: 47703 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 8.86 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K3B

1k3b


Resolution: 2.2→36.28 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / SU B: 13.488 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25475 2402 5.1 %RANDOM
Rwork0.21676 ---
obs0.21865 45153 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.003 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-1.16 Å20 Å2
2---1.16 Å20 Å2
3---3.78 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5535 0 114 115 5764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195855
X-RAY DIFFRACTIONr_bond_other_d0.0010.025218
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9417954
X-RAY DIFFRACTIONr_angle_other_deg0.753.00411968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62323.869274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86815875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6931522
X-RAY DIFFRACTIONr_chiral_restr0.0730.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026725
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021473
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_it1.2872.9312800
X-RAY DIFFRACTIONr_mcbond_other1.2872.9312799
X-RAY DIFFRACTIONr_mcangle_it2.064.933493
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7223.2023055
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: 2.204→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 174 -
Rwork0.297 3255 -
obs--98.65 %
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)
11.98150.29250.10042.69590.12031.15350.02080.0173-0.32220.0642-0.146-0.25530.24790.14510.12530.28660.08310.02490.09870.07670.162624.364245.819476.3187
21.72850.2146-0.19761.9399-0.0451.013-0.02770.0068-0.0196-0.0772-0.01990.45140.1677-0.16620.04750.2129-0.0831-0.040.07630.01380.2744-0.294651.284373.3907
31.43790.05820.20992.2731-0.52181.0448-0.0103-0.18380.07610.1717-0.0280.54880.2113-0.14040.03840.1993-0.11110.05140.1037-0.03040.2891-2.842554.501983.2146
43.5157-0.0736-0.08024.6922-0.07861.58980.11770.5911-0.0362-0.9253-0.11310.42520.0916-0.198-0.00460.44910.0521-0.09810.24970.00060.041810.29369.760346.6473
52.1107-1.2209-0.08473.0117-0.51230.64930.07110.25940.2005-0.4137-0.2505-0.74530.15330.09950.17940.29020.1510.18680.18350.11380.222134.850967.942753.0264
61.9615-0.65360.24343.4276-0.51310.88860.24390.28110.4059-0.3822-0.4248-1.12510.02160.19210.18090.21870.130.22050.15350.19560.427137.551878.048654.1769
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 120
2X-RAY DIFFRACTION2B206 - 367
3X-RAY DIFFRACTION3C372 - 439
4X-RAY DIFFRACTION4D1 - 118
5X-RAY DIFFRACTION5E205 - 367
6X-RAY DIFFRACTION6F372 - 439

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