6RN9 | pdb_00006rn9

DPP1 in complex with inhibitor

PDB DOI: https://doi.org/10.2210/pdb6RN9/pdb

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

Deposited: 2019-05-08 Released: 2019-08-28
Deposition Author(s): Kack, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.209 (Depositor), 0.203 (DCC)
R-Value Work:
0.185 (Depositor), 0.177 (DCC)
R-Value Observed:
0.186 (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

DPP1 Inhibitors: Exploring the Role of Water in the S2 Pocket of DPP1 with Substituted Pyrrolidines.

Kack, H., Doyle, K., Hughes, S.J., Bodnarchuk, M.S., Lonn, H., Van De Poel, A., Palmer, N.

(2019) ACS Med Chem Lett 10: 1222-1227

PubMed: 31413809 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.9b00261
Primary Citation Related Structures:
6RN6, 6RN7, 6RN9, 6RNE, 6RNI

PubMed Abstract:
A series of pyrrolidine amino nitrile DPP1 inhibitors have been developed and characterized. The S2 pocket structure-activity relationship for these compounds shows significant gains in potency for DPP1 from interacting further with target residues and a network of water molecules in the binding pocket. Herein we describe the X-ray crystal structures of several of these compounds alongside an analysis of factors influencing the inhibitory potency toward DPP1 of which stabilization of the water network, demonstrated using Grand Canonical Monte Carlo simulations and free energy calculations, is attributed as a main factor.

Organizational Affiliation

Structure, Biophysics and Fragments, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.

Macromolecule Content

Total Structure Weight: 41.2 kDa
Atom Count: 3,003
Modeled Residue Count: 347
Deposited Residue Count: 353
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 1	A	119	Homo sapiens	Mutation(s): 0 Gene Names: CTSC, CPPI EC: 3.4.14.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53634 (Homo sapiens) Explore P53634 Go to UniProtKB: P53634
PHAROS: P53634 GTEx: ENSG00000109861
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53634
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: P53634-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 1	B	165	Homo sapiens	Mutation(s): 0 Gene Names: CTSC, CPPI EC: 3.4.14.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53634 (Homo sapiens) Explore P53634 Go to UniProtKB: P53634
PHAROS: P53634 GTEx: ENSG00000109861
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53634
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B	Go to GlyGen: P53634-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 1	C	69	Homo sapiens	Mutation(s): 0 Gene Names: CTSC, CPPI EC: 3.4.14.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53634 (Homo sapiens) Explore P53634 Go to UniProtKB: P53634
PHAROS: P53634 GTEx: ENSG00000109861
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53634
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
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	2		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K9Z (Subject of Investigation/LOI) Query on K9Z Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	(2~{S},4~{S})-~{N}-[(2~{S})-1-azanyl-3-[4-(4-cyanophenyl)phenyl]propan-2-yl]-4-oxidanyl-pyrrolidine-2-carboxamide C₂₁ H₂₄ N₄ O₂ SNHLARAYZCCABX-UFYCRDLUSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.209 (Depositor), 0.203 (DCC)
R-Value Work: 0.185 (Depositor), 0.177 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.35	α = 90
b = 87.77	β = 90
c = 114.46	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-08-28

Deposition Author(s):

Kack, H.

Revision History (Full details and data files)

Version 1.0: 2019-08-28
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary