4W8D: PDB entry 4W8D

Crystal structure of MST3 with a pyrrolopyrimidine inhibitor (PF-06454589). Determined by X-ray diffraction at 1.77 Å resolution. Released 18 Mar 2015.

Method: X-ray diffraction
Resolution: 1.77 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,631
Mol. weight: 33.24 kDa
Ligands: 3JA
Released: 18 Mar 2015

Explore 4W8D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4W8D contains 18 α-helices and 14 β-strands across 1 chain. 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: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	1
α-helix	20-23	4
β-strand	24-33	10	1
β-strand	36-43	8	1
β-strand	49-56	8	1
α-helix	64-76	13
β-strand	82	1	2
β-strand	85-91	7	1
β-strand	94-100	7	1
β-strand	105-106	2	2
α-helix	107-110	4
α-helix	115-117	3
α-helix	118-137	20
β-strand	140-141	2	3
α-helix	147-149	3
β-strand	150-152	3	2
β-strand	158-160	3	2
β-strand	167-168	2	3
β-strand	176	1	4
α-helix	183-185	3
α-helix	188-191	4
β-strand	196	1	4
α-helix	199-214	16
α-helix	224-233	10
α-helix	235-237	3
α-helix	245-254	10
α-helix	259-261	3
α-helix	263-264	2
α-helix	265-268	4
α-helix	272-277	6
α-helix	281-284	4
α-helix	285-295	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase 24 36 kDa subunit	A	protein	290	Homo sapiens	Q9Y6E0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4W8D_1 Serine/threonine-protein kinase 24 36 kDa subunit (chains A)
GLPGMQNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAEDEIEDIQ
QEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREI
LKGLDYLHSEKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAP
EVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKVLFLIPKNNPPTLEGNYSKPLK
EFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDRYKRWKAEQ

Ligands and cofactors

ID	Name	Formula	Copies
3JA	5-(1-methyl-1H-pyrazol-4-yl)-4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidine	C14 H16 N6 O	1

Primary citation

Discovery and preclinical profiling of 3-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile (PF-06447475), a highly potent, selective, brain penetrant, and in vivo active LRRK2 kinase inhibitor. Henderson, J.L., Kormos, B.L., Hayward, M.M. et al. J Med Chem (2015) 58:419-432. DOI 10.1021/jm5014055 · 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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