3PDF
Discovery of Novel Cyanamide-Based Inhibitors of Cathepsin C
- PDB DOI: https://doi.org/10.2210/pdb3PDF/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): No 
- Deposited: 2010-10-22 Released: 2011-10-26 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.210 
- R-Value Work: 0.189 
- R-Value Observed: 0.190 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Dipeptidyl peptidase 1 | 441 | Homo sapiens | Mutation(s): 0  Gene Names: CTSC, CPPI EC: 3.4.14.1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P53634 (Homo sapiens) Explore P53634  Go to UniProtKB:  P53634 | |||||
PHAROS:  P53634 GTEx:  ENSG00000109861  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P53634 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
LXV Query on LXV | C [auth A] | 2,5-dibromo-N-{(3R,5S)-1-[(Z)-iminomethyl]-5-methylpyrrolidin-3-yl}benzenesulfonamide C12 H15 Br2 N3 O2 S HCQNBMQEPLAEIJ-NCAHPRJNSA-N | |||
NAG Query on NAG | D [auth A], E [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CL Query on CL | F [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.210 
- R-Value Work: 0.189 
- R-Value Observed: 0.190 
- Space Group: I 2 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 85.084 | α = 90 |
b = 88.784 | β = 90 |
c = 114.554 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
CNS | refinement |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |
Entry History 
Revision History (Full details and data files)
- Version 1.0: 2011-10-26
Type: Initial release - Version 1.1: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-07-26
Changes: Database references, Structure summary