2IIT
Human dipeptidyl peptidase 4 in complex with a diazepan-2-one inhibitor
- PDB DOI: https://doi.org/10.2210/pdb2IIT/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): Yes 
- Deposited: 2006-09-28 Released: 2006-11-28 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.35 Å
- R-Value Free: 0.228 
- R-Value Work: 0.188 
- R-Value Observed: 0.190 
This is version 2.2 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 4 soluble form | 728 | Homo sapiens | Mutation(s): 1  Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P27487 (Homo sapiens) Explore P27487  Go to UniProtKB:  P27487 | |||||
PHAROS:  P27487 GTEx:  ENSG00000197635  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P27487 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
872 Query on 872 | P [auth A], T [auth B] | (3R)-4-[(3R)-3-AMINO-4-(2,4,5-TRIFLUOROPHENYL)BUTANOYL]-3-(2,2,2-TRIFLUOROETHYL)-1,4-DIAZEPAN-2-ONE C17 H19 F6 N3 O2 RMDAPSXWBVPVOG-IAPIXIRKSA-N | |||
NAG Query on NAG | L [auth A] M [auth A] N [auth A] Q [auth B] R [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
NA Query on NA | O [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.35 Å
- R-Value Free: 0.228 
- R-Value Work: 0.188 
- R-Value Observed: 0.190 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 118.224 | α = 90 |
b = 125.197 | β = 90 |
c = 136.87 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
CNX | phasing |
CNX | refinement |
Entry History 
Deposition Data
- Released Date: 2006-11-28  Deposition Author(s): Scapin, G., Biftu, T., Weber, A.E.
Revision History (Full details and data files)
- Version 1.0: 2006-11-28
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2021-10-20
Changes: Database references, Structure summary - Version 2.2: 2023-08-30
Changes: Data collection, Refinement description