3N0T

Human dipeptidil peptidase DPP7 complexed with inhibitor GSK237826A

PDB DOI: https://doi.org/10.2210/pdb3N0T/pdb

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

Deposited: 2010-05-14 Released: 2010-07-21
Deposition Author(s): Dobrovetsky, E., Khutoreskaya, G., Seitova, A., Crombet, L., Cossar, D., Pagannon, S., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Hassell, A., Shewchuk, L., Haffner, C., Bochkarev, A., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.260 (Depositor), 0.280 (DCC)
R-Value Work:
0.218 (Depositor), 0.230 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Human dipeptidyl peptidase DPP7

Dobrovetsky, E., Khutoreskaya, G., Seitova, A., Crombet, L., Cossar, D., Pagannon, S., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Hassell, A., Shewchuk, L., Haffner, C., Bochkarev, A.

To be published.

Macromolecule Content

Total Structure Weight: 208.91 kDa
Atom Count: 14,133
Modelled Residue Count: 1,804
Deposited Residue Count: 1,876
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 2	A, B, C, D	469	Homo sapiens	Mutation(s): 0 Gene Names: DPP2, DPP7, QPP EC: 3.4.14.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHL4 (Homo sapiens) Explore Q9UHL4 Go to UniProtKB: Q9UHL4
PHAROS: Q9UHL4 GTEx: ENSG00000176978
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UHL4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OPY Query on OPY Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	(3S)-4-oxo-4-piperidin-1-ylbutane-1,3-diamine C₉ H₁₉ N₃ O RKBKYSFKXFKBBM-QMMMGPOBSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
OPY	BindingDB: 3N0T	IC50: min: 130, max: 1.91e+5 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.260 (Depositor), 0.280 (DCC)
R-Value Work: 0.218 (Depositor), 0.230 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.546	α = 90
b = 130.5	β = 102.28
c = 125.075	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
MOLREP	phasing
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-07-21

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-07-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary