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- PDB-4cdd: Human DPP1 in complex with (2S)-N-((1S)-1-cyano-2-(4-(4-cyanophen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cdd | |||||||||
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Title | Human DPP1 in complex with (2S)-N-((1S)-1-cyano-2-(4-(4-cyanophenyl) phenyl)ethyl)piperidine-2-carboxamide | |||||||||
![]() | (DIPEPTIDYL PEPTIDASE 1 ...) x 3 | |||||||||
![]() | HYDROLASE / INHIBITOR | |||||||||
Function / homology | ![]() 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 / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle ...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 / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle / : / phosphatase binding / cysteine-type peptidase activity / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of apoptotic signaling pathway / proteolysis involved in protein catabolic process / T cell mediated cytotoxicity / azurophil granule lumen / protein-folding chaperone binding / collagen-containing extracellular matrix / 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 | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Debreczeni, 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. | |||||||||
![]() | ![]() 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 |
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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 viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 293.6 KB | Display | ![]() |
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PDB format | ![]() | 240.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4cdcC ![]() 4cdeC ![]() 4cdfC ![]() 1k3bS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-DIPEPTIDYL PEPTIDASE 1 ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 13601.268 Da / Num. of mol.: 2 / Fragment: DPP1 EXCLUSION DOMAIN, RESIDUES 25-143 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 18630.018 Da / Num. of mol.: 2 / Fragment: DPP1 HEAVY CHAIN, RESIDUES 230-394 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 7583.444 Da / Num. of mol.: 2 / Fragment: DPP1 LIGHT CHAIN, RESIDUES 371-439 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar |
-Non-polymers , 3 types, 98 molecules ![](data/chem/img/GDI.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.81 % / Description: NONE |
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Crystal grow | Details: 21% PEG3350, 200MM AMSO4, 100MM NA ACCETATE PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() |
Detector | Detector: CCD / Date: May 31, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→44.1 Å / Num. obs: 38846 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1K3B Resolution: 2.35→44.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 14.103 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→44.07 Å
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Refine LS restraints |
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