PDB-9ijt: Crystal Structure of human Programmed cell death 1 ligand 1 (PD-L...

ID or keywords:

Entry

Database: PDB / ID: 9ijt

Title

Crystal Structure of human Programmed cell death 1 ligand 1 (PD-L1) bound to Small molecule inhibitor Compound-10

Components

Programmed cell death 1 ligand 1

Keywords

IMMUNE SYSTEM / Inhibitor

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 / negative regulation of type II interferon production ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Swaminathan, S. / Birudukota, S. / Vaithilingam, K. / Sadhu, N. / Gosu, R. / Rajagopal, S.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal Structure of human Programmed cell death 1 ligand 1 (PD-L1) bound to Small molecule inhibitor Compound-20
Authors: Swaminathan, S. / Birudukota, S. / Vaithilingam, K. / Sadhu, N. / Gosu, R. / Rajagopal, S.

History

Deposition	Jun 25, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 2, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9ijt.cif.gz	213.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9ijt.ent.gz		Display	PDB format
PDBx/mmJSON format	9ijt.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ij/9ijt ftp://data.pdbj.org/pub/pdb/validation_reports/ij/9ijt	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

hetero molecules

60.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	40.717, 85.206, 161.157
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	A
6	3	D
7	4	B
8	4	C
9	5	B
10	5	D
11	6	C
12	6	D

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: HIS / End label comp-ID: HIS

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	A	A	18 - 142	2 - 126
2	2	1	B	B	18 - 142	2 - 126
3	3	2	A	A	18 - 143	2 - 127
4	4	2	C	C	18 - 143	2 - 127
5	5	3	A	A	18 - 142	2 - 126
6	6	3	D	D	18 - 142	2 - 126
7	7	4	B	B	18 - 142	2 - 126
8	8	4	C	C	18 - 142	2 - 126
9	9	5	B	B	18 - 142	2 - 126
10	10	5	D	D	18 - 142	2 - 126
11	11	6	C	C	18 - 142	2 - 126
12	12	6	D	D	18 - 142	2 - 126

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

#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: 14811.928 Da / Num. of mol.: 4 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-A1L2P / (2~{S})-1-[[4-methoxy-2-[(2-methyl-3-phenyl-phenyl)methoxy]pyrimidin-5-yl]methyl]piperidine-2-carboxylic acid Mass: 447.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₆H₂₉N₃O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.36 Å³/Da / Density % sol: 47.86 %
Crystal grow	Temperature: 299 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris pH 8.5, 0.1M Magnesium chloride, 25% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953732 Å / Relative weight: 1
Reflection	Resolution: 2.05→45.44 Å / Num. obs: 36207 / % possible obs: 100 % / Redundancy: 13.2 % / CC_1/2: 0.999 / Net I/σ(I): 24.6
Reflection shell	Resolution: 2.05→2.11 Å / Num. unique obs: 2750 / CC_1/2: 0.958

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→45.44 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.928 / SU B: 11.446 / SU ML: 0.151 / Cross valid method: FREE R-VALUE / ESU R: 0.242 / ESU R Free: 0.192
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2601	1802	4.986 %
R_work	0.2311	34337	-
all	0.233	-	-
obs	-	36139	99.964 %

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: 48.133 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.157 Å²	0 Å²	-0 Å²
2-	-	-0.911 Å²	0 Å²
3-	-	-	-0.247 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→45.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4032	0	66	124	4222

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	4294
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4030
X-RAY DIFFRACTION	r_angle_refined_deg	1.504	1.66	5857
X-RAY DIFFRACTION	r_angle_other_deg	1.318	1.6	9271
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.949	5	541
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.813	22.825	223
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.486	15	729
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.03	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	559
X-RAY DIFFRACTION	r_chiral_restr_other	0.06	0.2	2
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5158
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1006
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	758
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	3887
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	2033
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2030
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.215	0.2	161
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.131	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.183	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.23	0.2	90
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.287	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.678	3.131	2062
X-RAY DIFFRACTION	r_mcbond_other	1.678	3.13	2061
X-RAY DIFFRACTION	r_mcangle_it	2.706	4.68	2580
X-RAY DIFFRACTION	r_mcangle_other	2.706	4.681	2581
X-RAY DIFFRACTION	r_scbond_it	1.868	3.393	2232
X-RAY DIFFRACTION	r_scbond_other	1.868	3.393	2233
X-RAY DIFFRACTION	r_scangle_it	2.985	4.992	3258
X-RAY DIFFRACTION	r_scangle_other	2.985	4.992	3259
X-RAY DIFFRACTION	r_lrange_it	7.262	59.72	17065
X-RAY DIFFRACTION	r_lrange_other	7.248	59.683	17036
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.158	0.05	3602
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.151	0.05	3688
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.154	0.05	3596
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.174	0.05	3587
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.154	0.05	3712
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.169	0.05	3554

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	0.15842	0.05007
1	2	B	X-RAY DIFFRACTION	Local ncs	0.15842	0.05007
2	3	A	X-RAY DIFFRACTION	Local ncs	0.15133	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.15133	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.15386	0.05007
3	6	D	X-RAY DIFFRACTION	Local ncs	0.15386	0.05007
4	7	B	X-RAY DIFFRACTION	Local ncs	0.17437	0.05008
4	8	C	X-RAY DIFFRACTION	Local ncs	0.17437	0.05008
5	9	B	X-RAY DIFFRACTION	Local ncs	0.15361	0.05008
5	10	D	X-RAY DIFFRACTION	Local ncs	0.15361	0.05008
6	11	C	X-RAY DIFFRACTION	Local ncs	0.16915	0.05007
6	12	D	X-RAY DIFFRACTION	Local ncs	0.16915	0.05007

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.05-2.103	0.334	133	0.287	2480	X-RAY DIFFRACTION	100
2.103-2.161	0.303	123	0.292	2437	X-RAY DIFFRACTION	99.961
2.161-2.223	0.273	140		2356	X-RAY DIFFRACTION	100
2.223-2.292	0.285	107	0.28	2305	X-RAY DIFFRACTION	100
2.292-2.367	0.306	114	0.259	2260	X-RAY DIFFRACTION	100
2.367-2.45	0.302	122	0.251	2125	X-RAY DIFFRACTION	100
2.45-2.542	0.304	99	0.26	2136	X-RAY DIFFRACTION	100
2.542-2.646	0.291	115	0.271	1976	X-RAY DIFFRACTION	100
2.646-2.764	0.289	93	0.257	1953	X-RAY DIFFRACTION	100
2.764-2.898	0.263	97	0.249	1870	X-RAY DIFFRACTION	100
2.898-3.055	0.324	92	0.255	1771	X-RAY DIFFRACTION	100
3.055-3.24	0.26	83	0.247	1673	X-RAY DIFFRACTION	100
3.24-3.463	0.25	82	0.247	1605	X-RAY DIFFRACTION	100
3.463-3.74	0.262	84	0.23	1478	X-RAY DIFFRACTION	99.936
3.74-4.096	0.24	74	0.2	1378	X-RAY DIFFRACTION	100
4.096-4.578	0.211	66	0.172	1248	X-RAY DIFFRACTION	100
4.578-5.283	0.191	58	0.178	1114	X-RAY DIFFRACTION	100
5.283-6.464	0.231	57	0.226	948	X-RAY DIFFRACTION	100
6.464-9.112	0.246	38	0.24	766	X-RAY DIFFRACTION	99.7519

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.4928	-2.7332	1.8012	5.4369	-2.5271	3.0449	-0.1714	-0.3714	-0.3545	-0.2281	0.394	0.4961	0.2745	-0.3384	-0.2226	0.1318	-0.0293	0.0256	0.1176	-0.0159	0.1427	1.1024	16.5017	11.0344
2	0.7607	0.0713	0.1138	6.8639	1.3265	1.4622	-0.1223	0.0661	-0.0411	-0.3435	0.2041	-0.5395	0.116	0.2128	-0.0819	0.0693	0.0082	0.036	0.0401	0.002	0.1244	15.6423	19.0691	31.4245
3	1.1861	-0.8488	-0.5679	7.5958	2.3937	2.3394	-0.0409	-0.0403	0.195	-0.4838	0.126	-0.2774	-0.4569	0.1704	-0.0851	0.3293	-0.001	-0.0195	0.1227	0.0273	0.1692	3.5536	53.6972	6.761
4	0.2951	-0.7694	0.1899	7.7869	-2.1597	1.6334	-0.0826	0.0557	0.024	-0.3115	0.2757	0.3607	-0.1498	-0.2736	-0.1931	0.1403	-0.018	0.0064	0.0843	0.0224	0.1335	3.9925	54.7326	32.2286

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	18 - 143
2	X-RAY DIFFRACTION	2	ALL	B	17 - 143
3	X-RAY DIFFRACTION	3	ALL	C	18 - 143
4	X-RAY DIFFRACTION	4	ALL	D	18 - 145

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