4CDC

Human DPP1 in complex with (2S)-2-amino-N-((1S)-1-cyano-2-(4- phenylphenyl)ethyl)butanamide

• PDB DOI: https://doi.org/10.2210/pdb4CDC/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-10-31 Released: 2014-03-19 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.233 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Starting Model: experimental

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

• PubMed: 24592859 
• 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.

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Organizational Affiliation: 

AstraZeneca , Pepparedsleden 1, Mölndal 431 83, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 162.15 kDa 
• Atom Count: 11,421 
• Modelled Residue Count: 1,373 
• Deposited Residue Count: 1,412 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN	A, D, G, J	119	Homo sapiens	Mutation(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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P53634-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN	B, E, H, K	165	Homo sapiens	Mutation(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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P53634-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN	C, F, I, L	69	Homo sapiens	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6AO	BA [auth K], N [auth B], S [auth E], X [auth H]	(2S)-2-azanyl-N-[(2S)-1-azanylidene-3-(4-phenylphenyl)propan-2-yl]butanamide C19 H23 N3 O ZXBGAEQZJOOPGZ-XYLSPAALSA-N
NAG	AA [auth J], CA [auth K], M [auth A], O [auth B], Q [auth D], U [auth G], Y [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	DA [auth K], R [auth D], V [auth G], W [auth G]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	EA [auth K], P [auth B], T [auth E], Z [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.233 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.276	α = 90
b = 84.276	β = 90
c = 224.626	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-19 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2014-03-19
  Type: Initial release
  
• Version 1.1: 2014-04-09
  Changes: Database references
• Version 1.2: 2019-04-24
  Changes: Data collection, Derived calculations, Other, Source and taxonomy
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.5: 2024-10-16
  Changes: Structure summary