4CDE

Human DPP1 in complex with 4-amino-N-((1S)-1-cyano-2-(4-(4- cyanophenyl)phenyl)ethyl)tetrahydropyran-4-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Cathepsin C Inhibitors: Property Optimization and Identification of a Clinical Candidate.

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.

(2014) J Med Chem 57: 2357

  • DOI: https://doi.org/10.1021/jm401705g
  • Primary Citation of Related Structures:  
    4CDC, 4CDD, 4CDE, 4CDF

  • PubMed Abstract: 

    A lead generation and optimization program delivered the highly selective and potent CatC inhibitor 10 as an in vivo tool compound and potential development candidate. Structural studies were undertaken to generate SAR understanding.


  • Organizational Affiliation

    AstraZeneca , Pepparedsleden 1, Mölndal 431 83, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN
A, D
119Homo sapiensMutation(s): 0 
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53634
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P53634-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN
B, E
165Homo sapiensMutation(s): 0 
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53634
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P53634-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN
C, F
69Homo sapiensMutation(s): 0 
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53634
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U6B
Query on U6B

Download Ideal Coordinates CCD File 
I [auth B],
N [auth F]
4-AZANYL-N-[(2S)-1-AZANYLIDENE-3-[4-(4-CYANOPHENYL)PHENYL]PROPAN-2-YL]OXANE-4-CARBOXAMIDE
C22 H24 N4 O2
DARWOCJYMDFZES-UDIPQKBFSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
K [auth D],
L [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth B],
M [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.35α = 90
b = 84.35β = 90
c = 224.94γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-04-09
    Changes: Database references
  • Version 1.2: 2017-03-29
    Changes: Other
  • Version 1.3: 2019-04-24
    Changes: Data collection, Derived calculations, Source and taxonomy
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.6: 2024-10-09
    Changes: Structure summary