6GL3: Human Phosphatidylinositol 4-kinase III beta

Crystal structure of human Phosphatidylinositol 4-kinase III beta (PI4KIIIbeta) in complex with ligand 44. Determined by X-ray diffraction at 2.77 Å resolution. Released 15 Aug 2018.

Method: X-ray diffraction
Resolution: 2.77 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,333
Mol. weight: 88.39 kDa
Ligands: EMW
Released: 15 Aug 2018

Explore 6GL3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GL3 contains 28 α-helices and 17 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: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	324-326	3
α-helix	327-339	13
α-helix	345-359	15
β-strand	376-380	5	1
α-helix	383-385	3
β-strand	387-388	2	1
α-helix	389-390	2
β-strand	397-405	9	1
α-helix	413-419	7
α-helix	537-547	11
β-strand	556-565	10	1
α-helix	570-588	19
β-strand	600-604	5	1
β-strand	607-610	4	1
α-helix	611-613	3
β-strand	616-618	3	2
α-helix	619-626	8
α-helix	630-637	8
α-helix	644-667	24
β-strand	677-680	4	2
β-strand	685-687	3	2
α-helix	712-717	6
α-helix	724-742	19
α-helix	744-755	12
α-helix	767-774	8
α-helix	782-796	15

Chain B: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	329-334	6
β-strand	376-380	5	3
β-strand	397-405	9	3
α-helix	537-547	11
β-strand	556-563	8	3
α-helix	570-588	19
β-strand	600-604	5	3
β-strand	607-610	4	3
β-strand	617-618	2	4
α-helix	619-626	8
α-helix	630-637	8
α-helix	644-667	24
β-strand	677-679	3	4
β-strand	685-687	3	4
α-helix	712-717	6
α-helix	724-742	19
α-helix	744-755	12
α-helix	762-774	13
α-helix	782-796	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta	A, B	protein	386	Homo sapiens	Q9UBF8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6GL3_1 Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta (chains A, B)
GSSPVRLAPEREFIKSLMAIGKRLATLPTKEQKTQRLISELSLLNHKLPARVWLPTAGFD
HHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFDTTSVPARIPENRIRSTRSDSGDGSA
LKEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLRQELLAFQVLKQLQSIWEQERVP
LWIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSLLDYFLQEHGSYTTEAFLSAQRN
FVQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDFGFILSSSPRNLGFETSAFKLTT
EFVDVMGGLDGDMFNYYKMLMLQGLIAARKHMDKVVQIVEIMQQGSQLPCFHGSSTIRNL
KERFHMSMTEEQLQLLVEQMVDGSMR

Ligands and cofactors

ID	Name	Formula	Copies
EMW	(3~{S})-4-(6-azanyl-1-methyl-pyrazolo[3,4-d]pyrimidin-4-yl)-~{N}-(4-methoxy-2-m…	C20 H26 N8 O2	1

Primary citation

Discovery of a Potent, Orally Bioavailable PI4KIII beta Inhibitor (UCB9608) Able To Significantly Prolong Allogeneic Organ Engraftment in Vivo. Reuberson, J., Horsley, H., Franklin, R.J. et al. J Med Chem (2018) 61:6705-6723. DOI 10.1021/acs.jmedchem.8b00521 · PubMed

Other PDB entries of the same protein (UniProt Q9UBF8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Q6F 1.51 Å, Human PI4KIIIB in complex with covalently bound inhibitor (compound 4)
8Q6G 1.54 Å, Human PI4KIIIB in complex with covalently bound inhibitor (compound 8)
8Q6H 1.94 Å, Human PI4KIIIB in complex with covalently bound inhibitor (compound 11)
5NAS 2.08 Å, Crystal structure of human 14-3-3 zeta in complex with PI4KIIIB peptide
5LX2 2.58 Å, Lt 14-3-3 in complex with PI4KIIIB peptide
5C46 2.65 Å, Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta…
4D0L 2.94 Å, Phosphatidylinositol 4-kinase III beta-PIK93 in a complex with Rab11a- GTP gammaS
8VOF 3.0 Å, GI targeted CpPI4K inhibitor
5C4G 3.2 Å, Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta…
5EUQ 3.2 Å, Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta…
5FBR 3.28 Å, PI4KB in complex with Rab11 and the MI359 Inhibitor
5FBV 3.29 Å, PI4KB in complex with Rab11 and the MI364 Inhibitor

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