5HI3

Binding site elucidation and structure guided design of macrocyclic IL-17A antagonists

PDB DOI: https://doi.org/10.2210/pdb5HI3/pdb

Classification: IMMUNE SYSTEM/INHIBITOR
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2016-01-11 Released: 2016-08-31
Deposition Author(s): Liu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.231
R-Value Work: 0.197
R-Value Observed: 0.199

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Binding site elucidation and structure guided design of macrocyclic IL-17A antagonists.

Liu, S., Dakin, L.A., Xing, L., Withka, J.M., Sahasrabudhe, P.V., Li, W., Banker, M.E., Balbo, P., Shanker, S., Chrunyk, B.A., Guo, Z., Chen, J.M., Young, J.A., Bai, G., Starr, J.T., Wright, S.W., Bussenius, J., Tan, S., Gopalsamy, A., Lefker, B.A., Vincent, F., Jones, L.H., Xu, H., Hoth, L.R., Geoghegan, K.F., Qiu, X., Bunnage, M.E., Thorarensen, A.

(2016) Sci Rep 6: 30859-30859

PubMed: 27527709 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/srep30859
Primary Citation of Related Structures:
5HI3, 5HI4, 5HI5

PubMed Abstract:
Interleukin-17A (IL-17A) is a principal driver of multiple inflammatory and immune disorders. Antibodies that neutralize IL-17A or its receptor (IL-17RA) deliver efficacy in autoimmune diseases, but no small-molecule IL-17A antagonists have yet progressed into clinical trials. Investigation of a series of linear peptide ligands to IL-17A and characterization of their binding site has enabled the design of novel macrocyclic ligands that are themselves potent IL-17A antagonists.

Organizational Affiliation

Worldwide Medicinal Chemistry, Pfizer Worldwide R&D, Eastern Point Road, Groton, CT 06340, USA.

Macromolecule Content

Total Structure Weight: 128.87 kDa
Atom Count: 8,343
Modelled Residue Count: 1,068
Deposited Residue Count: 1,182
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-17A	A, B	132	Homo sapiens	Mutation(s): 0 Gene Names: IL17A, CTLA8, IL17
UniProt & NIH Common Fund Data Resources
Find proteins for Q16552 (Homo sapiens) Explore Q16552 Go to UniProtKB: Q16552
PHAROS: Q16552 GTEx: ENSG00000112115
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16552
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CAT-2000 FAB heavy chain	C, E [auth H]	237	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CAT-2000 FAB light chain	D, G [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
synthetic IL-17A peptide inhibitor	F [auth I]	16	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
63O Query on 63O 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]	N-(4-{2-[({1-[2-(dimethylamino)-2-oxoethyl]cyclopentyl}acetyl)amino]ethyl}phenyl)-2-fluoro-Nalpha-[(1-methyl-1H-pyrazol-5-yl)carbonyl]-L-phenylalaninamide C₃₃ H₄₁ F N₆ O₄ VWRXSIAIHJZTCV-MHZLTWQESA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
63O	BindingDB: 5HI3	Kd: min: 660, max: 660 (nM) from 2 assay(s)
63O	BindingDB: 5HI3	IC50: 1140 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.231
R-Value Work: 0.197
R-Value Observed: 0.199
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.11	α = 90
b = 68.32	β = 90.82
c = 100.45	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data scaling
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-08-31

Deposition Author(s):

Liu, S.

Revision History (Full details and data files)

Version 1.0: 2016-08-31
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary