3D4L | pdb_00003d4l

Human dipeptidyl peptidase IV/CD26 in complex with a novel inhibitor

PDB DOI: https://doi.org/10.2210/pdb3D4L/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2008-05-14 Released: 2008-07-01
Deposition Author(s): Scapin, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.217 (Depositor), 0.214 (DCC)
R-Value Work:
0.192 (Depositor), 0.190 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Literature

Discovery of new binding elements in DPP-4 inhibition and their applications in novel DPP-4 inhibitor design.

Liang, G.B., Qian, X., Biftu, T., Singh, S., Gao, Y.D., Scapin, G., Patel, S., Leiting, B., Patel, R., Wu, J., Zhang, X., Thornberry, N.A., Weber, A.E.

(2008) Bioorg Med Chem Lett 18: 3706-3710

PubMed: 18524582 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.05.061
Primary Citation Related Structures:
3D4L

PubMed Abstract:
Probing with tool molecules, and by modeling and X-ray crystallography the binding modes of two structurally distinct series of DPP-4 inhibitors led to the discovery of a rare aromatic fluorine H-bond and the spatial requirement for better biaryl binding in the DPP-4 enzyme active site. These newly found binding elements were successfully incorporated into novel DPP-4 inhibitors.

Organizational Affiliation

gui-bai_liang@merck.comMerck Research Laboratories, Department of Medicinal Chemistry, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA.

Macromolecule Content

Total Structure Weight: 174.83 kDa
Atom Count: 13,340
Modeled Residue Count: 1,456
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4 soluble form	A, B	728	Homo sapiens	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27487
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P27487-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, F	2		N-Glycosylation	Interactions Focus chain C Focus chain F Interactions & Density Focus chain C Focus chain F
Glycosylation Resources
GlyTouCan: G07375KG GlyCosmos: G07375KG GlyGen: G07375KG

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
605 Query on 605 Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain P [auth A] mmCIF format, chain T [auth B] mmCIF format, chain P [auth A]	P [auth A], T [auth B]	4'-[(1R)-1-amino-2-(2,5-difluorophenyl)ethyl]biphenyl-3-carboxamide C₂₁ H₁₈ F₂ N₂ O JYKFWUXBFJJDTP-HXUWFJFHSA-N		Interactions Focus chain P [auth A] Focus chain T [auth B] Interactions & Density Focus chain P [auth A] Focus chain T [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Q [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth B]	L [auth A] M [auth A] N [auth A] Q [auth B] R [auth B] L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.217 (Depositor), 0.214 (DCC)
R-Value Work: 0.192 (Depositor), 0.190 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.435	α = 90
b = 125.749	β = 90
c = 137.175	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-07-01

Deposition Author(s):

Scapin, G.

Revision History (Full details and data files)

Version 1.0: 2008-07-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-10-20
Changes: Database references, Structure summary
Version 2.2: 2023-08-30
Changes: Data collection, Refinement description
Version 2.3: 2024-10-30
Changes: Structure summary