PDB-9o3b: PKM2 bound to MCTI-566

ID or keywords:

Entry

Database: PDB / ID: 9o3b

Title

PKM2 bound to MCTI-566

Components

Pyruvate kinase PKM

Keywords

TRANSFERASE / activator / pyruvate kinase

Function / homology

Function and homology information

pyruvate kinase / pyruvate kinase activity / programmed cell death / Pyruvate metabolism / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.416 Å

Authors

Stuckey, J.A.

Funding support

United States, 1items

Citation

Journal: Transl Vis Sci Technol / Year: 2025
Title: A Novel, Long-Acting, Small Molecule PKM2 Activator and Its Potential Broad Application Against Photoreceptor Degeneration.
Authors: Pan, W.W. / Weh, K.M. / Chaudhury, S. / Fernando, R. / Hager, H. / Wen, B. / Chinnaswamy, K. / Stuckey, J.A. / Rech, J.C. / Besirli, C.G. / Weh, E. / Wubben, T.J.

History

Deposition	Apr 7, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 13, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9o3b.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb9o3b.ent.gz		Display	PDB format
PDBx/mmJSON format	9o3b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9o3b_validation.pdf.gz	3.3 MB	Display	wwPDB validaton report
Full document	9o3b_full_validation.pdf.gz	3.3 MB	Display
Data in XML	9o3b_validation.xml.gz	166.5 KB	Display
Data in CIF	9o3b_validation.cif.gz	218.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o3/9o3b ftp://data.pdbj.org/pub/pdb/validation_reports/o3/9o3b	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	#50 - Feb 2004 Glycolytic Enzymes similarity (15) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1)

Deposited unit

A: Pyruvate kinase PKM

B: Pyruvate kinase PKM

C: Pyruvate kinase PKM

D: Pyruvate kinase PKM

E: Pyruvate kinase PKM

F: Pyruvate kinase PKM

G: Pyruvate kinase PKM

H: Pyruvate kinase PKM

hetero molecules

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

1

A: Pyruvate kinase PKM

B: Pyruvate kinase PKM

C: Pyruvate kinase PKM

D: Pyruvate kinase PKM

hetero molecules

defined by author&software
Evidence: gel filtration
242 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Pyruvate kinase PKM

F: Pyruvate kinase PKM

G: Pyruvate kinase PKM

H: Pyruvate kinase PKM

hetero molecules

defined by author&software
242 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.807, 93.855, 153.660
Angle α, β, γ (deg.)	89.73, 89.68, 75.79
Int Tables number	1
Space group name H-M	P1

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Protein / Sugars , 2 types, 12 molecules ABCDEFGH

#1: Protein

Pyruvate kinase PKM / Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate ...

Mass: 60050.102 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Production host:

Escherichia coli (E. coli) / References: UniProt: P14618, pyruvate kinase

#2: Sugar

ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose

Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₁₂P₂

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Non-polymers , 6 types, 1198 molecules

#3: Chemical	ChemComp-OXL / OXALATE ION Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂O₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-A1B77 / 7-[(dimethylamino)methyl]-8-fluoro-5-methyl-3-[(6-methylpyridin-2-yl)methyl]-3,5-dihydro-4H-pyridazino[4,5-b]indol-4-one Mass: 379.431 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₂FN₅O / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1172 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.11 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 5 uL of protein complex solution and 5 uL of well solution containing 0.1 M MES pH 6.5 and 25% polyethylene glycol 6000.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MAR CCD 300 mm / Detector: CCD / Date: Dec 15, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.416→50 Å / Num. obs: 165005 / % possible obs: 98.6 % / Redundancy: 3.9 % / B_iso Wilson estimate: 45.55 Å² / CC_1/2: 0.991 / CC star: 0.998 / R_merge(I) obs: 0.072 / R_pim(I) all: 0.042 / R_rim(I) all: 0.084 / Χ²: 0.82 / Net I/σ(I): 9.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.42-2.46	3.8	0.922	8245	0.607	0.869	0.542	1.071	0.78	97.8
2.46-2.51	3.8	0.759	8208	0.696	0.906	0.446	0.881	0.787	97.9
2.51-2.55	3.8	0.649	8169	0.758	0.929	0.381	0.753	0.802	98
2.55-2.61	3.9	0.567	8262	0.797	0.942	0.332	0.658	0.826	98
2.61-2.66	3.9	0.477	8107	0.852	0.959	0.279	0.552	0.82	98
2.66-2.73	3.9	0.405	8217	0.884	0.969	0.237	0.47	0.855	98.2
2.73-2.79	3.9	0.32	8239	0.919	0.979	0.187	0.371	0.881	98.2
2.79-2.87	3.9	0.279	8193	0.935	0.983	0.163	0.323	0.886	98.3
2.87-2.95	3.9	0.226	8231	0.955	0.988	0.132	0.262	0.907	98.4
2.95-3.05	3.9	0.181	8275	0.965	0.991	0.106	0.21	0.954	98.5
3.05-3.16	3.9	0.146	8247	0.976	0.994	0.085	0.169	0.953	98.7
3.16-3.28	4	0.113	8262	0.982	0.995	0.065	0.13	0.967	98.7
3.28-3.43	4	0.087	8249	0.987	0.997	0.05	0.1	0.994	98.8
3.43-3.61	4	0.07	8327	0.99	0.997	0.041	0.081	1.011	98.9
3.61-3.84	3.9	0.058	8315	0.991	0.998	0.034	0.067	1.036	99.1
3.84-4.14	3.9	0.046	8238	0.993	0.998	0.027	0.053	0.888	99.1
4.14-4.55	3.9	0.035	8267	0.995	0.999	0.021	0.041	0.697	98.9
4.55-5.21	3.9	0.03	8315	0.996	0.999	0.018	0.035	0.549	99.3
5.21-6.56	3.8	0.027	8309	0.995	0.999	0.016	0.032	0.436	99.5
6.56-50	3.8	0.022	8330	0.997	0.999	0.013	0.026	0.334	99.3

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Processing

Software

Name	Version	Classification
BUSTER	2.10.4 (8-JUN-2022)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
MOLREP		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.416→45.49 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.92 / SU R Cruickshank DPI: 0.501 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.454 / SU R_free Blow DPI: 0.246 / SU R_free Cruickshank DPI: 0.253
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2263	7818	5.02 %	RANDOM
R_work	0.1858	-	-	-
obs	0.1878	155831	92.9 %	-

Displacement parameters

B_iso mean: 49.46 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.8586 Å²	0.982 Å²	0.8423 Å²
2-	-	2.8301 Å²	0.7964 Å²
3-	-	-	-3.6887 Å²

Refine analyze

Luzzati coordinate error obs: 0.28 Å

Refinement step

Cycle: LAST / Resolution: 2.416→45.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30397	0	268	1172	31837

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.007	31591	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	0.9	43122	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		10782	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes
X-RAY DIFFRACTION	t_gen_planes		5637	HARMONIC	5
X-RAY DIFFRACTION	t_it		31294	HARMONIC	10
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	2.73
X-RAY DIFFRACTION	t_other_torsion	16.32
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		4310	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		26510	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.42→2.45 Å / Total num. of bins used: 51

	R_factor	Num. reflection	% reflection
R_free	0.3305	135	4.33 %
R_work	0.2488	2982	-
all	0.2525	3117	-
obs	-	-	51.4 %

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	1.2329	-0.0297	0.13	0.9836	-0.1946	0.5833	0.2853	0.1098	0.3684	-0.1461	-0.0538	0.1472	-0.3442	-0.0235	-0.2315	0.002	0.1	0.0816	-0.0517	0.0731	0.006	-24.9722	25.1287	6.735
2	7.2669	1.3118	-0.1531	11.5968	7.172	18.5334	-0.0452	-1.6817	-0.1061	0.8497	-0.0894	0.6015	0.3428	-0.808	0.1346	-0.4307	-0.0371	0.1836	0.5804	-0.0461	-0.4347	-29.0718	18.7927	42.1056
3	1.1699	-0.1132	-0.3419	0.3692	0.3626	0.9403	0.1694	0.1341	0.1148	-0.1105	-0.0641	0.1439	-0.0925	-0.1449	-0.1053	-0.0453	0.0696	0.0032	0.0255	0.0756	0.0106	-25.1361	13.7497	4.4998
4	2.1311	0.5256	0.1948	0.8052	0.6413	0.9841	0.2505	-0.437	0.173	0.0711	0.0382	0.018	0.0283	0.0486	-0.2887	-0.0697	-0.0266	0.1114	0.0853	-0.091	-0.078	4.3862	18.4092	31.1563
5	5.4074	1.9378	0.7732	5.2338	1.0877	1.9791	-0.0817	0.1244	1.63	-0.258	-0.0558	0.8459	-0.6153	0.2189	0.1375	-0.1284	0.0136	0.2282	-0.4226	0.1467	0.7068	-1.7006	51.0009	11.1034
6	1.2679	-0.1908	-0.0391	0.785	0.0117	0.2951	0.2081	-0.2298	0.1725	0.0027	-0.0677	-0.0331	-0.0319	0.1332	-0.1404	-0.0945	-0.0518	0.0998	0.0894	-0.0405	-0.0141	10.6459	15.6589	21.7886
7	1.159	-0.5184	0.527	1.1195	0.0813	0.6511	0.151	0.212	-0.3111	-0.3538	-0.112	0.1476	0.039	-0.4033	-0.039	0.1754	0.0177	-0.0054	0.0152	-0.1355	-0.2123	-3.8851	-16.988	-30.5568
8	4.6394	0.2368	-0.452	8.4	0.6339	5.781	0.2232	0.1829	0.0363	-0.1998	-0.13	-0.5551	-0.6158	0.6866	-0.0931	-0.1081	-0.0762	0.151	0.0876	-0.0495	-0.1912	31.1894	-19.1803	-39.8831
9	0.9265	-0.5365	-0.3312	0.9558	-0.1226	0.5998	0.0327	0.2506	-0.0161	-0.4343	-0.0961	0.0139	0.0586	-0.2446	0.0634	0.183	0.0592	-0.0173	0.0696	-0.0314	-0.1989	-2.6564	-6.3512	-27.6141
10	0.3734	-0.9604	0.2846	2.5536	-0.425	2.44	-0.0479	0.1344	0.1708	-0.1593	-0.0406	-0.4387	0.4858	0.4042	0.0885	0.0906	0.1714	0.119	-0.1146	0.0131	-0.0498	24.3908	-25.4641	-5.9293
11	7.2204	0.193	-0.6815	8.2377	1.4173	6.8183	0.1079	0.5398	-0.815	-0.5289	-0.0905	0.4225	0.9461	-0.4519	-0.0174	0.566	-0.4054	0.1175	-0.3632	-0.1388	-0.2514	-5.9972	-48.6403	-15.6196
12	0.2687	0.1912	0.1539	1.3412	0.8326	1.6407	-0.0157	-0.09	-0.0628	0.0529	-0.0647	-0.2397	0.4392	0.1042	0.0804	0.1356	0.0828	0.085	-0.0802	0.0555	-0.0649	16.9527	-22.919	2.1566
13	2.0526	0.3769	-0.212	0.4866	-0.3199	0.8199	0.2364	-0.4294	-0.1559	0.0796	0.0238	-0.0423	-0.0301	-0.0329	-0.2602	-0.0814	-0.0174	-0.099	0.0911	0.1092	-0.0756	-33.0267	26.8628	-45.5841
14	7.8884	-0.092	-0.4324	9.3107	0.0803	2.9346	-0.1926	-0.059	-1.6675	-0.3151	0.011	-0.8697	0.6621	-0.1183	0.1817	-0.1742	0.0082	-0.1196	-0.4764	-0.0995	0.6741	-27.0957	-5.7641	-65.7147
15	1.2379	-0.1284	0.0277	0.7605	0.0188	0.298	0.2026	-0.2238	-0.1902	0.0067	-0.0399	0.036	0.0159	-0.1188	-0.1628	-0.0926	-0.0343	-0.0926	0.0881	0.0708	-0.0153	-39.3436	29.6055	-54.9075
16	1.7549	0.1959	-0.0373	0.6188	0.069	0.5464	0.291	0.1298	-0.425	-0.1265	-0.0802	-0.1353	0.3074	0.0128	-0.2108	0.0063	0.1164	-0.1052	-0.0439	-0.078	0.0056	-3.7937	20.0939	-70.0756
17	6.4832	0.0562	0.8693	9.7121	-7.0623	18.2833	-0.0521	-1.5531	0.0557	0.7163	-0.1558	-0.4438	-0.3889	0.841	0.2079	-0.4596	-0.0313	-0.1282	0.6289	0.1519	-0.4071	0.5818	26.6102	-34.7512
18	1.0898	-0.1127	0.2526	0.4227	-0.398	0.6735	0.1769	0.1164	-0.107	-0.1223	-0.06	-0.1245	0.0802	0.1262	-0.117	-0.0258	0.0762	-0.0152	0.0296	-0.0644	-0.0044	-3.6852	31.442	-72.4156
19	0.8343	-1.063	-0.2683	2.3206	0.1385	2.1337	-0.0265	0.1098	-0.1552	-0.0892	-0.04	0.4221	-0.4499	-0.3679	0.0664	0.1057	0.1849	-0.0959	-0.1034	-0.0065	-0.0922	-53.2833	70.5914	-82.6463
20	6.0693	0.568	-0.3256	8.0724	-1.4942	4.8002	0.081	0.4457	0.7153	-0.4896	-0.1619	-0.3872	-0.9557	0.4974	0.0809	0.5787	-0.3998	-0.0558	-0.3615	0.158	-0.2156	-22.985	93.7621	-92.5483
21	0.2995	0.1622	-0.1872	1.1889	-0.7758	1.5857	-0.0165	-0.1028	0.044	0.0652	-0.0405	0.2283	-0.4359	-0.1133	0.057	0.1448	0.089	-0.0661	-0.083	-0.0367	-0.0615	-45.8791	67.9336	-74.4948
22	1.1344	-0.3847	-0.5164	1.0483	0.0347	0.6168	0.0635	0.2128	0.3072	-0.3035	-0.1018	-0.0812	-0.0941	0.4126	0.0384	0.1231	0.0154	-0.0048	0.0488	0.1496	-0.2023	-25.2061	61.8689	-107.2635
23	5.5524	0.9392	-0.2823	8.0897	-0.7899	4.8015	0.2084	0.2883	0.0195	-0.152	-0.0171	0.5377	0.5792	-0.5471	-0.1913	-0.0965	-0.0668	-0.1415	0.073	0.0896	-0.2022	-60.4558	64.0501	-116.5153
24	0.8435	-0.5317	0.2551	0.97	0.2039	0.5411	0.0678	0.2294	0.0101	-0.4421	-0.0938	-0.0329	-0.0987	0.2046	0.026	0.1817	0.0632	0.0159	0.0634	0.0224	-0.1916	-26.3824	51.3329	-104.469

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{A\|13 - 117}
2	X-RAY DIFFRACTION	2	{A\|118 - 217}
3	X-RAY DIFFRACTION	3	{A\|218 - 531}
4	X-RAY DIFFRACTION	4	{B\|14 - 117}
5	X-RAY DIFFRACTION	5	{B\|118 - 217}
6	X-RAY DIFFRACTION	6	{B\|218 - 531}
7	X-RAY DIFFRACTION	7	{C\|11 - 117}
8	X-RAY DIFFRACTION	8	{C\|118 - 217}
9	X-RAY DIFFRACTION	9	{C\|218 - 531}
10	X-RAY DIFFRACTION	10	{D\|14 - 117}
11	X-RAY DIFFRACTION	11	{D\|118 - 217}
12	X-RAY DIFFRACTION	12	{D\|218 - 531}
13	X-RAY DIFFRACTION	13	{E\|14 - 117}
14	X-RAY DIFFRACTION	14	{E\|118 - 217}
15	X-RAY DIFFRACTION	15	{E\|218 - 531}
16	X-RAY DIFFRACTION	16	{F\|13 - 117}
17	X-RAY DIFFRACTION	17	{F\|118 - 217}
18	X-RAY DIFFRACTION	18	{F\|218 - 531}
19	X-RAY DIFFRACTION	19	{G\|14 - 117}
20	X-RAY DIFFRACTION	20	{G\|118 - 217}
21	X-RAY DIFFRACTION	21	{G\|218 - 531}
22	X-RAY DIFFRACTION	22	{H\|11 - 117}
23	X-RAY DIFFRACTION	23	{H\|118 - 217}
24	X-RAY DIFFRACTION	24	{H\|218 - 531}

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