3G0G

Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinone inhibitor 3

PDB DOI: https://doi.org/10.2210/pdb3G0G/pdb

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

Deposited: 2009-01-27 Released: 2010-02-16
Deposition Author(s): Zhang, Z., Wallace, M.B., Feng, J., Stafford, J.A., Kaldor, S.W., Shi, L., Skene, R.J., Aertgeerts, K., Lee, B., Jennings, A., Xu, R., Kassel, D., Webb, D.R., Gwaltney, S.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.265
R-Value Work: 0.210
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 351.59 kDa
Atom Count: 24,783
Modelled Residue Count: 2,868
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
Sequence Annotations Expand
Reference Sequence

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 E, F, G, H, I, J, K, L	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RUM Query on RUM Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain BA [auth D] SDF format, chain M [auth A] SDF format, chain W [auth C] MOL2 format, chain R [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain W [auth C]	BA [auth D], M [auth A], R [auth B], W [auth C]	2-({2-[(3R)-3-aminopiperidin-1-yl]-5-bromo-6-oxopyrimidin-1(6H)-yl}methyl)benzonitrile C₁₇ H₁₈ Br N₅ O GGCILSXUAHLDMF-CQSZACIVSA-N		Interactions Focus chain BA [auth D] Focus chain M [auth A] Focus chain R [auth B] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain M [auth A] Focus chain R [auth B] Focus chain W [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	AA [auth C] CA [auth D] DA [auth D] EA [auth D] FA [auth D] AA [auth C], CA [auth D], DA [auth D], EA [auth D], FA [auth D], N [auth A], O [auth A], P [auth A], Q [auth A], S [auth B], T [auth B], U [auth B], V [auth B], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
RUM	BindingDB: 3G0G	IC50: 5 (nM) from 1 assay(s)
	PDBBind: 3G0G	IC50: 5 (nM) from 1 assay(s)
	Binding MOAD: 3G0G	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.265
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.906	α = 90
b = 122.921	β = 114.77
c = 145.092	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-02-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-02-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-11-01
Changes: Advisory, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

3G0G

Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinone inhibitor 3

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)