8QLR: Human MST3 (STK24) kinase

Human MST3 (STK24) kinase in complex with inhibitor MR24. Determined by X-ray diffraction at 1.85 Å resolution. Released 8 Nov 2023.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,328
Mol. weight: 70.32 kDa
Ligands: VYN
Released: 8 Nov 2023

Explore 8QLR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QLR contains 37 α-helices and 20 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	3
α-helix	32-35	4
β-strand	36-44	9	3
β-strand	49-55	7	3
β-strand	61-68	8	3
α-helix	76-88	13
β-strand	94	1	4
α-helix	95-96	2
β-strand	97-103	7	3
β-strand	106-112	7	3
β-strand	118	1	4
α-helix	119-122	4
α-helix	127-129	3
α-helix	130-149	20
α-helix	159-161	3
β-strand	162-164	3	4
β-strand	170-172	3	4
α-helix	175-177	3
α-helix	200-203	4
α-helix	211-226	16
α-helix	236-245	10
α-helix	247-249	3
α-helix	257-266	10
α-helix	271-273	3
α-helix	275-276	2
α-helix	277-280	4
α-helix	284-289	6
α-helix	293-295	3
α-helix	296-301	6

Chain B: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	1
α-helix	32-35	4
β-strand	36-44	9	1
β-strand	48-55	8	1
β-strand	60-68	9	1
α-helix	76-87	12
β-strand	94	1	2
α-helix	95-96	2
β-strand	97-103	7	1
β-strand	106-111	6	1
β-strand	117-118	2	2
α-helix	119-122	4
α-helix	127-129	3
α-helix	130-149	20
α-helix	159-161	3
β-strand	162-164	3	2
β-strand	170-172	3	2
α-helix	200-204	5
α-helix	211-226	16
α-helix	236-245	10
α-helix	247-249	3
α-helix	257-266	10
α-helix	271-273	3
α-helix	275-276	2
α-helix	277-280	4
α-helix	284-289	6
α-helix	293-296	4
α-helix	297-303	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase 24	A, B	protein	306	Homo sapiens	Q9Y6E0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8QLR_1 Serine/threonine-protein kinase 24 (chains A, B)
MRAQLWGLALNKRRATLPHPGGSTNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQKVV
AIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDL
LEPGPLDETQIATILREILKGLDYLHSEKKIHRDIKAANVLLSEHGEVKLADFGVAGQLT
DTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKVLFL
IPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDA
HHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
VYN	8-(4-azanylbutyl)-2-[1,3-bis(oxidanyl)propan-2-ylamino]-6-[2-chloranyl-4-(6-met…	C26 H29 Cl N6 O3	2

Water and common crystallization additives (EDO) are not listed.

Primary citation

Development of Selective Pyrido[2,3- d ]pyrimidin-7(8 H )-one-Based Mammalian STE20-Like (MST3/4) Kinase Inhibitors. Rak, M., Menge, A., Tesch, R. et al. J Med Chem (2024) 67:3813-3842. DOI 10.1021/acs.jmedchem.3c02217 · PubMed

Other PDB entries of the same protein (UniProt Q9Y6E0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3A7I 1.45 Å, Human MST3 kinase in complex with adenine
8QLT 1.47 Å, Human MST3 (STK24) kinase in complex with inhibitor MR30
3A7J 1.5 Å, Human MST3 kinase in complex with MnADP
4QMT 1.5 Å, MST3 in complex with HESPERADIN
4QMU 1.55 Å, MST3 in complex with jnj-7706621, 4-({5-amino-1-[(2,6-difluorophenyl)carbonyl]-1H-1,2,4-t…
3A7F 1.55 Å, Human MST3 kinase
4QMW 1.6 Å, MST3 in complex with pp-121, 1-cyclopentyl-3-(1H-PYRROLO[2,3-b]pyridin-5-yl)-1H-PYRAZOLO[…
8QLS 1.61 Å, Human MST3 (STK24) kinase in complex with inhibitor MR26
4U8Z 1.63 Å, Crystal structure of MST3 with a pyrrolopyrimidine inhibitor (PF-06447475)
8QLQ 1.64 Å, Human MST3 (STK24) kinase in complex with macrocyclic inhibitor JA310
8BZI 1.72 Å, Human MST3 (STK24) kinase in complex with inhibitor MR39
7B32 1.75 Å, MST3 in complex with MRIA7

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