PDB-6plg: Crystal structure of human PHGDH complexed with Compound 15

ID or keywords:

Entry

Database: PDB / ID: 6plg

Title

Crystal structure of human PHGDH complexed with Compound 15

Components

D-3-phosphoglycerate dehydrogenase

Keywords

OXIDOREDUCTASE/INHIBITOR / DEHYDROGENASE / SERINE METABOLISM / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex

Function / homology

Function and homology information

threonine metabolic process / 2-oxoglutarate reductase / gamma-aminobutyric acid metabolic process / glial cell development / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / taurine metabolic process / Serine biosynthesis / glycine metabolic process / L-serine biosynthetic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.93 Å

Authors

Olland, A. / Lakshminarasimhan, D. / White, A. / Suto, R.K.

Citation

Journal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Inhibition of 3-phosphoglycerate dehydrogenase (PHGDH) by indole amides abrogates de novo serine synthesis in cancer cells.
Authors: Mullarky, E. / Xu, J. / Robin, A.D. / Huggins, D.J. / Jennings, A. / Noguchi, N. / Olland, A. / Lakshminarasimhan, D. / Miller, M. / Tomita, D. / Michino, M. / Su, T. / Zhang, G. / Stamford, ...

History

Deposition	Jun 30, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 24, 2019	Provider: repository / Type: Initial release
Revision 1.1	Aug 7, 2019	Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Sep 4, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6plg.cif.gz	905 KB	Display	PDBx/mmCIF format
PDB format	pdb6plg.ent.gz	791.8 KB	Display	PDB format
PDBx/mmJSON format	6plg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6plg_validation.pdf.gz	2.6 MB	Display	wwPDB validaton report
Full document	6plg_full_validation.pdf.gz	2.7 MB	Display
Data in XML	6plg_validation.xml.gz	87.9 KB	Display
Data in CIF	6plg_validation.cif.gz	114.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pl/6plg ftp://data.pdbj.org/pub/pdb/validation_reports/pl/6plg	HTTPS FTP

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Related structure data

Related structure data	6plfC C: citing same article (ref.)
Similar structure data	6rj2-d 6rih-d 4g2n-2 1wwk-d 1j4a-1 1gdh-d 5uog-1 1j49-d 5j23-2 2dld-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6plfC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (2) #21 - Sep 2001 Antibodies similarity (1)

Deposited unit

A: D-3-phosphoglycerate dehydrogenase

B: D-3-phosphoglycerate dehydrogenase

C: D-3-phosphoglycerate dehydrogenase

D: D-3-phosphoglycerate dehydrogenase

E: D-3-phosphoglycerate dehydrogenase

F: D-3-phosphoglycerate dehydrogenase

G: D-3-phosphoglycerate dehydrogenase

H: D-3-phosphoglycerate dehydrogenase

hetero molecules

274 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: D-3-phosphoglycerate dehydrogenase

E: D-3-phosphoglycerate dehydrogenase

hetero molecules

defined by author&software
68.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: D-3-phosphoglycerate dehydrogenase

F: D-3-phosphoglycerate dehydrogenase

hetero molecules

defined by author&software
68.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: D-3-phosphoglycerate dehydrogenase

G: D-3-phosphoglycerate dehydrogenase

hetero molecules

defined by author&software
68.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: D-3-phosphoglycerate dehydrogenase

H: D-3-phosphoglycerate dehydrogenase

hetero molecules

defined by author&software
68.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	44.649, 112.699, 137.840
Angle α, β, γ (deg.)	105.980, 96.200, 101.420
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	6 - 308
2	1	B	6 - 308
1	2	A	6 - 308
2	2	C	6 - 308
1	3	A	6 - 308
2	3	D	6 - 308
1	4	A	7 - 307
2	4	E	7 - 307
1	5	A	9 - 306
2	5	F	9 - 306
1	6	A	6 - 306
2	6	G	6 - 306
1	7	A	6 - 308
2	7	H	6 - 308
1	8	B	6 - 308
2	8	C	6 - 308
1	9	B	6 - 308
2	9	D	6 - 308
1	10	B	7 - 307
2	10	E	7 - 307
1	11	B	9 - 306
2	11	F	9 - 306
1	12	B	6 - 306
2	12	G	6 - 306
1	13	B	6 - 308
2	13	H	6 - 308
1	14	C	6 - 308
2	14	D	6 - 308
1	15	C	7 - 307
2	15	E	7 - 307
1	16	C	9 - 306
2	16	F	9 - 306
1	17	C	6 - 306
2	17	G	6 - 306
1	18	C	6 - 308
2	18	H	6 - 308
1	19	D	7 - 307
2	19	E	7 - 307
1	20	D	9 - 306
2	20	F	9 - 306
1	21	D	6 - 306
2	21	G	6 - 306
1	22	D	6 - 308
2	22	H	6 - 308
1	23	E	9 - 306
2	23	F	9 - 306
1	24	E	7 - 306
2	24	G	7 - 306
1	25	E	7 - 307
2	25	H	7 - 307
1	26	F	9 - 306
2	26	G	9 - 306
1	27	F	9 - 306
2	27	H	9 - 306
1	28	G	6 - 306
2	28	H	6 - 306

NCS ensembles :

#1: Protein	D-3-phosphoglycerate dehydrogenase / 3-PGDH / 2-oxoglutarate reductase / Malate dehydrogenase Mass: 33630.762 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PHGDH, PGDH3 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O43175, phosphoglycerate dehydrogenase, 2-oxoglutarate reductase, malate dehydrogenase
#2: Chemical	ChemComp-ONS / (2S)-(4-{3-[(4,5-dichloro-1-methyl-1H-indole-2-carbonyl)amino]oxetan-3-yl}phenyl)(pyridin-3-yl)acetic acid Mass: 510.369 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₆H₂₁Cl₂N₃O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₆O₅
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: 2.39 Å³/Da / Density % sol: 48.6 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 27% PEG mme 5000, 180 mM ammonium sulfate, 90 mM MES pH 6.5, 2% glycerol, and 20 mM DL-malic acid pH 7.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID30B / Wavelength: 0.97625 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.97625 Å / Relative weight: 1

Reflection

Resolution: 2.93→50 Å / Num. obs: 49500 / % possible obs: 93.3 % / Redundancy: 1.7 % / R_merge(I) obs: 0.099 / R_pim(I) all: 0.099 / R_rim(I) all: 0.14 / Χ²: 1.004 / Net I/σ(I): 6.8 / Num. measured all: 83204

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	Χ²	% possible all
2.93-3.03	1.7	0.577	4939	0.75	0.577	0.816	1.002	93.5
3.03-3.16	1.6	0.448	4983	0.828	0.448	0.634	1.001	93.3
3.16-3.3	1.7	0.345	4922	0.852	0.345	0.488	1.017	93.2
3.3-3.47	1.6	0.292	4847	0.937	0.292	0.413	1.006	91.2
3.47-3.69	1.8	0.178	4847	0.977	0.178	0.252	1.005	90.5
3.69-3.98	1.7	0.149	4820	0.966	0.149	0.21	1.008	91.5
3.98-4.38	1.7	0.085	4978	0.982	0.085	0.121	0.997	93.9
4.38-5.01	1.7	0.062	5093	0.989	0.062	0.087	0.992	95.6
5.01-6.31	1.7	0.058	5058	0.99	0.058	0.083	1.012	95.1
6.31-50	1.7	0.032	5013	0.997	0.032	0.046	1.001	94.7

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
REFMAC	5.8.0253	refinement
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.93→45.42 Å / Cor.coef. F_o:F_c: 0.907 / Cor.coef. F_o:F_c free: 0.87 / SU B: 108.792 / SU ML: 0.826 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.6
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3148	2339	4.7 %	RANDOM
R_work	0.2742	-	-	-
obs	0.2761	47083	92.63 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 225.09 Å² / B_iso mean: 99.666 Å² / B_iso min: 58.74 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.57 Å²	1.38 Å²	0.96 Å²
2-	-	4.83 Å²	3.94 Å²
3-	-	-	-3.55 Å²

Refinement step

Cycle: final / Resolution: 2.93→45.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17938	0	316	0	18254
B_iso mean	-	-	91.34	-	-
Num. residues	-	-	-	-	2418

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	18490
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	17629
X-RAY DIFFRACTION	r_angle_refined_deg	1.766	1.663	25056
X-RAY DIFFRACTION	r_angle_other_deg	1.217	1.588	40881
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.036	5	2410
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.74	22.818	841
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.424	15	3237
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.801	15	125
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	2502
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	20768
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3499

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	8427	0.12
1	2	B	8427	0.12
2	1	A	8626	0.09
2	2	C	8626	0.09
3	1	A	8575	0.09
3	2	D	8575	0.09
4	1	A	8414	0.11
4	2	E	8414	0.11
5	1	A	8347	0.1
5	2	F	8347	0.1
6	1	A	8290	0.11
6	2	G	8290	0.11
7	1	A	8532	0.1
7	2	H	8532	0.1
8	1	B	8498	0.11
8	2	C	8498	0.11
9	1	B	8435	0.11
9	2	D	8435	0.11
10	1	B	8299	0.12
10	2	E	8299	0.12
11	1	B	8226	0.12
11	2	F	8226	0.12
12	1	B	8236	0.12
12	2	G	8236	0.12
13	1	B	8425	0.12
13	2	H	8425	0.12
14	1	C	8858	0.05
14	2	D	8858	0.05
15	1	C	8586	0.08
15	2	E	8586	0.08
16	1	C	8524	0.07
16	2	F	8524	0.07
17	1	C	8504	0.09
17	2	G	8504	0.09
18	1	C	8774	0.07
18	2	H	8774	0.07
19	1	D	8515	0.09
19	2	E	8515	0.09
20	1	D	8464	0.08
20	2	F	8464	0.08
21	1	D	8453	0.09
21	2	G	8453	0.09
22	1	D	8688	0.08
22	2	H	8688	0.08
23	1	E	8503	0.08
23	2	F	8503	0.08
24	1	E	8385	0.1
24	2	G	8385	0.1
25	1	E	8603	0.08
25	2	H	8603	0.08
26	1	F	8373	0.1
26	2	G	8373	0.1
27	1	F	8547	0.08
27	2	H	8547	0.08
28	1	G	8601	0.08
28	2	H	8601	0.08

LS refinement shell

Resolution: 2.934→3.01 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.367	156	-
R_work	0.371	3272	-
all	-	3428	-
obs	-	-	87.38 %

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	2.4068	1.4371	0.9081	1.0861	1.0814	5.3681	-0.0801	0.2078	0.0191	-0.0845	0.346	0.22	0.071	-0.2218	-0.2659	1.0806	-0.1135	-0.0788	0.4173	0.2927	1.3591	-14.664	6.535	-68.561
2	1.4606	-0.7248	-0.7885	0.7817	1.676	4.5865	0.0973	-0.5074	-0.0044	0.0165	0.1679	0.1066	-0.0485	-0.0583	-0.2652	1.7243	-0.0034	0.2557	0.4538	0.3686	1.6079	-14.448	9.829	71.949
3	3.4932	0.7544	1.2268	5.6421	-2.5415	4.3761	-0.0559	0.0667	0.0077	-0.6273	0.2925	-0.1791	0.2091	0.1183	-0.2365	0.8841	0.0465	0.0432	0.3292	-0.2311	0.7606	-26.509	93.878	-53.665
4	2.5849	-1.0908	-0.6728	4.3535	-2.3722	4.7199	-0.23	0.2193	-0.0739	0.6571	0.2757	-0.0626	-0.1713	0.1571	-0.0456	1.0393	-0.1205	-0.0143	0.2013	-0.2127	0.9208	-4.172	33.34	56.903
5	5.0057	0.5071	0.6718	3.8405	-0.0974	3.6109	-0.1325	-0.8734	0.261	-0.2993	-0.2301	0.0166	-0.0863	-0.1035	0.3627	1.0701	0.193	0.2708	0.2347	-0.2081	0.9358	-25.511	29.261	-4.78
6	4.5917	-3.3331	0.2762	4.4968	-0.1883	3.6978	-0.39	0.8043	-0.2654	0.6016	-0.4387	-0.1882	-0.2545	-0.5573	0.8287	1.2219	-0.2746	-0.3757	0.3182	-0.2034	1.2319	-25.812	-12.437	8.773
7	0.9174	1.0034	-1.1425	7.2237	-0.3212	1.7266	0.1508	-0.1399	-0.236	-0.0638	-0.1334	-0.0511	-0.0832	0.1332	-0.0175	1.0864	0.2268	0.1027	0.7142	0.0759	1.0573	-7.354	52.551	-3.794
8	0.5881	-0.8506	0.7154	6.3215	-0.2353	3.0886	0.1421	0.3163	0.1264	-0.0482	-0.2223	-0.0823	-0.0821	0.0856	0.0803	1.1085	-0.3292	-0.0639	0.6079	0.0789	0.8159	14.51	74.562	6.436
9	1.3143	0.9114	-0.5479	2.6639	0.3184	2.0168	-0.0064	0.2428	0.5305	0.5114	0.4767	1.1495	0.0217	0.1436	-0.4703	1.0118	0.176	0.3496	0.1195	0.1608	1.598	-20.477	4.644	-35.814
10	1.0485	-0.7887	0.0597	3.1993	0.7244	1.5738	-0.0706	-0.1267	-0.3651	-0.4308	0.4734	1.218	0.0386	0.3132	-0.4029	0.9678	-0.2465	-0.3418	0.1577	0.1353	1.6527	-20.455	12.328	39.318
11	0.9461	0.1344	0.0802	3.2444	-0.4172	1.207	-0.3026	-0.2606	-0.0478	0.3241	0.2006	0.0892	-0.2311	0.0858	0.102	0.957	0.2793	0.0832	0.2315	-0.1857	0.8342	-15.372	86.96	-22.291
12	0.7849	0.7121	0.6364	3.7987	0.5605	1.5945	-0.3601	0.1965	0.0211	-0.3399	0.2694	0.0713	0.1543	0.0453	0.0907	1.0231	-0.3654	-0.0347	0.1916	-0.1874	0.8405	6.947	40.296	25.639
13	0.9791	0.7667	1.4353	3.3832	0.1855	2.5734	-0.0891	0.3218	0.1562	0.4901	0.4933	1.4972	-0.0145	0.4614	-0.4042	1.1399	0.2419	0.5443	0.1766	0.2097	1.8353	-15.814	28.882	-35.355
14	0.4559	0.1681	-1.1205	3.1743	0.3219	3.0982	-0.1786	-0.1532	0.1048	-0.503	0.4252	1.2442	0.0662	0.5841	-0.2466	1.1207	-0.2888	-0.4874	0.2124	0.1603	1.8322	-15.819	-12.14	38.731
15	1.7466	-0.1678	-0.4779	2.3535	-0.3924	0.8733	-0.4715	-0.4022	-0.3821	0.0508	0.2341	0.2269	0.1761	0.2392	0.2374	1.147	0.227	0.2084	0.2136	-0.0764	1.1863	-20.554	63.715	-29.615
16	2.1606	0.1897	0.5136	1.704	-1.2421	1.7281	-0.3874	0.3363	0.5115	-0.1853	0.2197	0.3281	0.0601	0.1461	0.1676	1.1896	-0.3462	-0.2512	0.3033	-0.0631	1.3079	1.744	63.646	32.855

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 101
2	X-RAY DIFFRACTION	1	A	289 - 308
3	X-RAY DIFFRACTION	2	B	6 - 101
4	X-RAY DIFFRACTION	2	B	289 - 308
5	X-RAY DIFFRACTION	3	C	6 - 101
6	X-RAY DIFFRACTION	3	C	289 - 308
7	X-RAY DIFFRACTION	4	D	6 - 101
8	X-RAY DIFFRACTION	4	D	289 - 308
9	X-RAY DIFFRACTION	5	E	7 - 101
10	X-RAY DIFFRACTION	5	E	289 - 308
11	X-RAY DIFFRACTION	6	F	9 - 101
12	X-RAY DIFFRACTION	6	F	289 - 307
13	X-RAY DIFFRACTION	7	G	6 - 101
14	X-RAY DIFFRACTION	7	G	289 - 307
15	X-RAY DIFFRACTION	8	H	6 - 101
16	X-RAY DIFFRACTION	8	H	289 - 308
17	X-RAY DIFFRACTION	9	A	102 - 288
18	X-RAY DIFFRACTION	10	B	102 - 288
19	X-RAY DIFFRACTION	11	C	102 - 288
20	X-RAY DIFFRACTION	12	D	102 - 288
21	X-RAY DIFFRACTION	13	E	102 - 288
22	X-RAY DIFFRACTION	14	F	102 - 288
23	X-RAY DIFFRACTION	15	G	102 - 288
24	X-RAY DIFFRACTION	16	H	102 - 288

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