4G1F

Crystal Structure of human Dipeptidyl Peptidase IV in complex with a pyridopyrimidinedione analogue

PDB DOI: https://doi.org/10.2210/pdb4G1F/pdb

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

Deposited: 2012-07-10 Released: 2013-02-27
Deposition Author(s): Skene, R.J., Gwaltney, S.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.207 (Depositor), 0.210 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Structure-based design of pyridopyrimidinediones as dipeptidyl peptidase IV inhibitors.

Lam, B., Zhang, Z., Stafford, J.A., Skene, R.J., Shi, L., Gwaltney, S.L.

(2012) Bioorg Med Chem Lett 22: 6628-6631

PubMed: 23025999 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2012.08.110
Primary Citation of Related Structures:
4G1F

PubMed Abstract:
Dipeptidyl peptidase IV (DPP-4) inhibitors have been shown to enhance GLP-1 levels and thereby improve hyperglycemia in type II diabetes. From a small fragment hit, using structure-based design, we have discovered a new class of non-covalent, potent and selective DPP-4 inhibitors.

Organizational Affiliation

Takeda California, 10410 Science Center Drive, San Diego, CA 92121, USA. blam@takedasd.com

Macromolecule Content

Total Structure Weight: 349.44 kDa
Atom Count: 24,443
Modelled Residue Count: 2,888
Deposited Residue Count: 2,960
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 4	A, B, C, D	740	Homo sapiens	Mutation(s): 0 Gene Names: ADCP2, CD26, DPP4 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
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P27487-1
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H, I	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0WG Query on 0WG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain W [auth D] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D]	J [auth A], O [auth B], T [auth C], W [auth D]	7-amino-6-(aminomethyl)-5-(2-bromophenyl)-1,3-dimethylpyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione C₁₆ H₁₆ Br N₅ O₂ JGBNONXELAWFNR-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain W [auth D] Interactions & Density Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain W [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	K [auth A] L [auth A] M [auth A] N [auth A] P [auth B] K [auth A], L [auth A], M [auth A], N [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], U [auth C], V [auth C], X [auth D], Y [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
0WG	BindingDB: 4G1F	IC50: 17 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.259 (Depositor), 0.260 (DCC)
R-Value Work: 0.207 (Depositor), 0.210 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.622	α = 90
b = 121.362	β = 114.63
c = 143.257	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-02-27

Deposition Author(s):

Skene, R.J.

Gwaltney, S.L.

Revision History (Full details and data files)

Version 1.0: 2013-02-27
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary