4CDF

Human DPP1 in complex with (2S,4S)-N-((1S)-1-cyano-2-(4-(4- cyanophenyl)phenyl)ethyl)-4-hydroxy-piperidine-2-carboxamide

Structural Biology Knowledgebase: 4CDF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.217

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4CDF

Classification: HYDROLASE

Total Structure Weight: 81565.08

Macromolecule Entities
Molecule Chains Length Organism Details
DIPEPTIDYL PEPTIDASE 1 EXCLUSION DOMAIN CHAIN A, D 120 Homo sapiens EC#: 3.4.14.1 IUBMB
Fragment: DPP1 EXCLUSION DOMAIN, RESIDUES 25-144
Gene Name(s): CTSC Gene View CPPI
DIPEPTIDYL PEPTIDASE 1 HEAVY CHAIN B, E 166 Homo sapiens EC#: 3.4.14.1 IUBMB
Fragment: DPP1 HEAVY CHAIN, RESIDUES 229-394
Gene Name(s): CTSC Gene View CPPI
DIPEPTIDYL PEPTIDASE 1 LIGHT CHAIN C, F 69 Homo sapiens EC#: 3.4.14.1 IUBMB
Gene Name(s): CTSC Gene View CPPI

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
W2C
Query on W2C

B, E (2S,4S)-N-[(2S)-1-azanylidene-3-[4-(4-cyanophenyl)phenyl]propan- 2-yl]-4-oxidanyl-piperidine-2-carboxamide
C22 H24 N4 O2
IOCQAXABAZCRSK-QCXLXSPFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B, D, E N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B, E CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.217
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 84.85 α = 90.00
b = 84.85 β = 90.00
c = 222.45 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-10-31
  • 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

  • 2014-04-09
    Type: Citation | Details: JRNL