2JID | pdb_00002jid

Human Dipeptidyl peptidase IV in complex with 1-(3,4-Dimethoxy-phenyl) -3-m-tolyl-piperidine-4-ylamine

PDB DOI: https://doi.org/10.2210/pdb2JID/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2007-02-28 Released: 2008-05-27
Deposition Author(s): Hennig, M., Stihle, M., Luebbers, T., Thoma, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.303 (Depositor)
R-Value Work:
0.223 (Depositor)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

1,3-Disubstituted 4-Aminopiperidines as Useful Tools in the Optimization of the 2-Aminobenzo[A]Quinolizine Dipeptidyl Peptidase Iv Inhibitors.

Lubbers, T., Bohringer, M., Gobbi, L., Hennig, M., Hunziker, D., Kuhn, B., Loffler, B., Mattei, P., Narquizian, R., Peters, J., Ruff, Y., Wessel, H.P., Wyss, P.

(2007) Bioorg Med Chem Lett 17: 2966

PubMed: 17418568 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2007.03.072
Primary Citation Related Structures:
2JID

PubMed Abstract:
In a search for novel DPP-IV inhibitors, 2-aminobenzo[a]quinolizines were identified as submicromolar HTS hits. Due to the difficult synthetic access to this compound class, 1,3-disubstituted 4-aminopiperidines were used as model compounds for optimization. The developed synthetic methodology and the SAR could be transferred to the 2-aminobenzo[a]quinolizine series, leading to highly active DPP-IV inhibitors.

Organizational Affiliation

Discovery Research, Pharmaceutical Division, F. Hoffmann-La Roche Ltd, CH-4070 Basel, Switzerland. thomas.luebbers@roche.com

Macromolecule Content

Total Structure Weight: 172.84 kDa
Atom Count: 12,214
Modeled Residue Count: 1,456
Deposited Residue Count: 1,472
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIPEPTIDYL PEPTIDASE 4	A, B	736	Homo sapiens	Mutation(s): 0 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27487
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P27487-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GVB Query on GVB Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	(3R,4S)-1-(3,4-DIMETHOXYPHENYL)-3-(3-METHYLPHENYL)PIPERIDIN-4-AMINE C₂₀ H₂₆ N₂ O₂ DQJXBZGPJVSWFI-ROUUACIJSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth B] C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
GVB	BindingDB: 2JID	IC50: 600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.303 (Depositor)
R-Value Work: 0.223 (Depositor)
R-Value Observed: 0.227 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.251	α = 90
b = 66.821	β = 90
c = 423.948	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-05-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-05-27
Type: Initial release
Version 1.1: 2012-08-29
Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Structure summary