PDB-9eo0: Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed D...

ID or keywords:

Entry

Database: PDB / ID: 9eo0

Title

Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1

Components

Programmed cell death 1 ligand 1

Keywords

ANTITUMOR PROTEIN / PD-L1 / SMI / Nonsymmetrically

Function / homology

Function and homology information

negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Plewka, J. / Hec, A. / Sitar, T. / Holak, T.

Funding support

Poland, 1items

Citation

Journal: Acs Med.Chem.Lett. / Year: 2024
Title: Nonsymmetrically Substituted 1,1'-Biphenyl-Based Small Molecule Inhibitors of the PD-1/PD-L1 Interaction.
Authors: Hec-Galazka, A. / Tyrcha, U. / Barczynski, J. / Bielski, P. / Mikitiuk, M. / Gudz, G.P. / Kitel, R. / Musielak, B. / Plewka, J. / Sitar, T. / Holak, T.A.

History

Deposition	Mar 14, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 19, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 3, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9eo0.cif.gz	289 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9eo0_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	9eo0_full_validation.pdf.gz	1 MB	Display
Data in XML	9eo0_validation.xml.gz	28.1 KB	Display
Data in CIF	9eo0_validation.cif.gz	37.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eo/9eo0 ftp://data.pdbj.org/pub/pdb/validation_reports/eo/9eo0	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#204 - Dec 2016 PD-1 similarity (4) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (2) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (3) #20 - Aug 2001 Poliovirus and Rhinovirus similarity (2) #231 - Mar 2019 Measles Virus Proteins similarity (2) #63 - Mar 2005 T-Cell Receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (1) #209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#204 - Dec 2016
PD-1
similarity (4)
#186 - Jun 2015
Receptor for Advanced Glycation End Products
similarity (2)
#247 - Jul 2020
Myelin-associated Glycoprotein
similarity (3)
#20 - Aug 2001
Poliovirus and Rhinovirus
similarity (2)
#231 - Mar 2019
Measles Virus Proteins
similarity (2)
#63 - Mar 2005
T-Cell Receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#169 - Jan 2014
HIV Envelope Glycoprotein
similarity (1)
#209 - May 2017
Tissue Transglutaminase and Celiac Disease
similarity (1)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (1)

Deposited unit

A: Programmed cell death 1 ligand 1

B: Programmed cell death 1 ligand 1

C: Programmed cell death 1 ligand 1

D: Programmed cell death 1 ligand 1

E: Programmed cell death 1 ligand 1

F: Programmed cell death 1 ligand 1

hetero molecules

91.8 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Programmed cell death 1 ligand 1

B: Programmed cell death 1 ligand 1

hetero molecules

defined by author
30.6 kDa, 2 polymers

2

C: Programmed cell death 1 ligand 1

F: Programmed cell death 1 ligand 1

hetero molecules

defined by author
30.7 kDa, 2 polymers

3

D: Programmed cell death 1 ligand 1

E: Programmed cell death 1 ligand 1

hetero molecules

defined by author
30.6 kDa, 2 polymers

Unit cell

Length a, b, c (Å)	70.753, 75.405, 75.923
Angle α, β, γ (deg.)	90, 97.249, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	TYR	TYR	4 - 120	4 - 120
2	1	1	ALA	ALA	TYR	TYR	4 - 120	4 - 120
3	2	2	SER	SER	TYR	TYR	3 - 120	3 - 120
4	2	2	SER	SER	TYR	TYR	3 - 120	3 - 120
5	3	3	ALA	ALA	ALA	ALA	4 - 121	4 - 121
6	3	3	ALA	ALA	ALA	ALA	4 - 121	4 - 121
7	4	4	ALA	ALA	PRO	PRO	4 - 119	4 - 119
8	4	4	ALA	ALA	PRO	PRO	4 - 119	4 - 119
9	5	5	ALA	ALA	TYR	TYR	4 - 120	4 - 120
10	5	5	ALA	ALA	TYR	TYR	4 - 120	4 - 120
11	6	6	ALA	ALA	TYR	TYR	4 - 120	4 - 120
12	6	6	ALA	ALA	TYR	TYR	4 - 120	4 - 120
13	7	7	ALA	ALA	TYR	TYR	4 - 120	4 - 120
14	7	7	ALA	ALA	TYR	TYR	4 - 120	4 - 120
15	8	8	ALA	ALA	PRO	PRO	4 - 119	4 - 119
16	8	8	ALA	ALA	PRO	PRO	4 - 119	4 - 119
17	9	9	ALA	ALA	ALA	ALA	4 - 121	4 - 121
18	9	9	ALA	ALA	ALA	ALA	4 - 121	4 - 121
19	10	10	ALA	ALA	TYR	TYR	4 - 120	4 - 120
20	10	10	ALA	ALA	TYR	TYR	4 - 120	4 - 120
21	11	11	ALA	ALA	PRO	PRO	4 - 119	4 - 119
22	11	11	ALA	ALA	PRO	PRO	4 - 119	4 - 119
23	12	12	ALA	ALA	TYR	TYR	4 - 120	4 - 120
24	12	12	ALA	ALA	TYR	TYR	4 - 120	4 - 120
25	13	13	ALA	ALA	PRO	PRO	4 - 119	4 - 119
26	13	13	ALA	ALA	PRO	PRO	4 - 119	4 - 119
27	14	14	ALA	ALA	TYR	TYR	4 - 120	4 - 120
28	14	14	ALA	ALA	TYR	TYR	4 - 120	4 - 120
29	15	15	ALA	ALA	PRO	PRO	4 - 119	4 - 119
30	15	15	ALA	ALA	PRO	PRO	4 - 119	4 - 119

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1 Mass: 14954.085 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#2: Chemical	ChemComp-A1H56 / ~{N}-[3-[3-[[5-[(2-hydroxyethylamino)methyl]pyridin-2-yl]carbonylamino]-2-methyl-phenyl]-2-methyl-phenyl]-5-[[3-(methylsulfonylamino)propylamino]methyl]pyridine-2-carboxamide Mass: 659.798 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃₄H₄₁N₇O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.07 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium HEPES 7.5 25 % w/v PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, DESY

/ Beamline: P11 / Wavelength: 1.03322 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.03322 Å / Relative weight: 1

Reflection

Resolution: 2.5→48.39 Å / Num. obs: 27366 / % possible obs: 99.2 % / Redundancy: 7.1 % / CC_1/2: 0.997 / R_merge(I) obs: 0.148 / R_pim(I) all: 0.091 / R_rim(I) all: 0.174 / Net I/σ(I): 6.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
9.01-48.39	6.8	0.049	628	0.997	0.03	0.058
2.5-2.6	7.3	2.112	3124	0.695	1.278	2.474

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→44.393 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.916 / SU B: 19.939 / SU ML: 0.398 / Cross valid method: FREE R-VALUE / ESU R: 0.96 / ESU R Free: 0.366
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3025	1380	5.046 %
R_work	0.253	25971	-
all	0.256	-	-
obs	-	27351	99.058 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 64.368 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.536 Å²	-0 Å²	-4.097 Å²
2-	-	3.138 Å²	-0 Å²
3-	-	-	-1.511 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→44.393 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5655	0	146	32	5833

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	5911
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	5609
X-RAY DIFFRACTION	r_angle_refined_deg	1.766	1.826	8006
X-RAY DIFFRACTION	r_angle_other_deg	0.766	1.761	12877
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.056	5	705
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.965	9.412	51
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.974	10	1016
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.879	10	269
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	889
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	6855
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1351
X-RAY DIFFRACTION	r_nbd_refined	0.178	0.2	858
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.159	0.2	4871
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	2735
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	3229
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.349	0.2	136
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.072	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.216	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.157	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.093	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	5.842	6.239	2838
X-RAY DIFFRACTION	r_mcbond_other	5.818	6.24	2838
X-RAY DIFFRACTION	r_mcangle_it	9.002	11.218	3537
X-RAY DIFFRACTION	r_mcangle_other	9.002	11.221	3538
X-RAY DIFFRACTION	r_scbond_it	6.071	6.683	3073
X-RAY DIFFRACTION	r_scbond_other	6.045	6.651	3070
X-RAY DIFFRACTION	r_scangle_it	9.655	12.142	4469
X-RAY DIFFRACTION	r_scangle_other	9.612	12.085	4464
X-RAY DIFFRACTION	r_lrange_it	15.452	64.971	6113
X-RAY DIFFRACTION	r_lrange_other	15.451	64.968	6114
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.099	0.05	3356
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.113	0.05	3354
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.126	0.05	3281
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.123	0.05	3278
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.13	0.05	3269
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.101	0.05	3346
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.109	0.05	3304
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.127	0.05	3273
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.139	0.05	3260
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.089	0.05	3373
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.119	0.05	3278
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.126	0.05	3269
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.122	0.05	3255
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.137	0.05	3250
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.112	0.05	3325

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09871	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09871	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.11312	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.11312	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.12606	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.12606	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.12276	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.12276	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.1297	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.1297	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.10065	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.10065	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.10912	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.10912	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.12668	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.12668	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.13934	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.13934	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.08918	0.05011
10	20	A	X-RAY DIFFRACTION	Local ncs	0.08918	0.05011
11	21	A	X-RAY DIFFRACTION	Local ncs	0.11925	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.11925	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.12574	0.05009
12	24	A	X-RAY DIFFRACTION	Local ncs	0.12574	0.05009
13	25	A	X-RAY DIFFRACTION	Local ncs	0.12183	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.12183	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.13677	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.13677	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.11152	0.05011
15	30	A	X-RAY DIFFRACTION	Local ncs	0.11152	0.05011

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.5-2.565	0.415	110	0.436	1923	0.434	2036	0.859	0.847	99.8527	0.418
2.565-2.635	0.486	101	0.411	1865	0.415	1971	0.837	0.863	99.7463	0.395
2.635-2.711	0.364	99	0.38	1816	0.379	1925	0.892	0.892	99.4805	0.364
2.711-2.794	0.421	82	0.356	1768	0.359	1856	0.865	0.91	99.6767	0.337
2.794-2.885	0.333	90	0.322	1692	0.322	1793	0.923	0.929	99.3865	0.293
2.885-2.986	0.278	81	0.293	1652	0.292	1744	0.941	0.946	99.3693	0.264
2.986-3.098	0.386	99	0.295	1585	0.3	1695	0.902	0.948	99.351	0.269
3.098-3.224	0.378	79	0.292	1545	0.296	1636	0.904	0.947	99.2665	0.266
3.224-3.367	0.295	63	0.273	1458	0.274	1555	0.943	0.956	97.8135	0.252
3.367-3.53	0.364	61	0.26	1371	0.264	1506	0.919	0.96	95.0863	0.243
3.53-3.72	0.261	53	0.254	1368	0.254	1423	0.951	0.962	99.8595	0.239
3.72-3.943	0.365	64	0.244	1281	0.25	1347	0.93	0.964	99.8515	0.232
3.943-4.213	0.314	75	0.225	1196	0.23	1273	0.941	0.972	99.8429	0.219
4.213-4.548	0.232	64	0.193	1088	0.195	1164	0.962	0.98	98.9691	0.192
4.548-4.976	0.267	69	0.184	1030	0.19	1107	0.97	0.984	99.2773	0.188
4.976-5.555	0.248	53	0.184	921	0.187	986	0.971	0.985	98.783	0.191
5.555-6.398	0.262	45	0.182	829	0.187	889	0.971	0.984	98.3127	0.184
6.398-7.795	0.253	55	0.213	664	0.217	743	0.97	0.976	96.7699	0.215
7.795-10.858	0.246	24	0.2	574	0.202	598	0.973	0.984	100	0.212
10.858-44.393	0.198	13	0.274	345	0.271	358	0.976	0.961	100	0.291

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