3CCB

Crystal Structure of Human DPP4 in complex with a benzimidazole derivative

PDB DOI: https://doi.org/10.2210/pdb3CCB/pdb

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

Deposited: 2008-02-25 Released: 2008-10-21
Deposition Author(s): Wallace, M.B., Skene, R.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.244 (Depositor), 0.270 (DCC)
R-Value Work:
0.200 (Depositor), 0.234 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure-based design and synthesis of benzimidazole derivatives as dipeptidyl peptidase IV inhibitors.

Wallace, M.B., Feng, J., Zhang, Z., Skene, R.J., Shi, L., Caster, C.L., Kassel, D.B., Xu, R., Gwaltney, S.L.

(2008) Bioorg Med Chem Lett 18: 2362-2367

PubMed: 18346892 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.02.071
Primary Citation of Related Structures:
3CCB, 3CCC

PubMed Abstract:
A novel series of non-covalent, benzimidazole-based inhibitors of DPP-4 has been developed from a small fragment hit using structure-based drug design. A highly versatile synthetic route was created for the development of SAR, which led to the discovery of potent and selective inhibitors with excellent pharmaceutical properties.

Organizational Affiliation

Takeda San Diego, Drug Discovery, 10410 Science Center Drive, San Diego, CA 92121, USA. michael.wallace@takedasd.com

Macromolecule Content

Total Structure Weight: 348.61 kDa
Atom Count: 24,805
Modelled Residue Count: 2,901
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: 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
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
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	J [auth A] K [auth A] L [auth A] M [auth A] O [auth B] J [auth A], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], T [auth C], U [auth C], W [auth D], X [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D]
B2Y Query on B2Y Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain S [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain N [auth A] mmCIF format, chain S [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D]	N [auth A], S [auth B], V [auth C], Y [auth D]	1-biphenyl-2-ylmethanamine C₁₃ H₁₃ N YHXKXVFQHWJYOD-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain S [auth B] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain N [auth A] Focus chain S [auth B] Focus chain V [auth C] Focus chain Y [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
B2Y	BindingDB: 3CCB	IC50: 3.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.244 (Depositor), 0.270 (DCC)
R-Value Work: 0.200 (Depositor), 0.234 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.086	α = 90
b = 123.01	β = 114.84
c = 144.651	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-10-21

Deposition Author(s):

Wallace, M.B.

Skene, R.J.

Revision History (Full details and data files)

Version 1.0: 2008-10-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-25
Changes: 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: 2024-10-30
Changes: Data collection, Database references, Structure summary