5TBM: PT2385

Crystal structure of PT2385 bound to HIF2a-B*:ARNT-B* complex. Determined by X-ray diffraction at 1.85 Å resolution. Released 21 Sept 2016.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,824
Mol. weight: 27.43 kDa
Ligands: 79A
Released: 21 Sept 2016

Explore 5TBM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TBM contains 13 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: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	240-242	3
β-strand	243-248	6	1
β-strand	253	1	2
β-strand	254-257	4	1
α-helix	259-261	3
α-helix	262-265	4
α-helix	269-271	3
β-strand	276	1	2
α-helix	277-279	3
β-strand	281	1	1
α-helix	283-285	3
α-helix	286-299	14
β-strand	301-303	3	1
β-strand	307-310	4	1
β-strand	316-326	11	1
β-strand	336-343	8	1

Chain B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	359-361	3
β-strand	362-367	6	3
β-strand	372	1	4
β-strand	373-376	4	3
α-helix	380-384	5
α-helix	388-391	4
β-strand	395	1	4
α-helix	396-399	4
β-strand	400	1	3
α-helix	405-415	11
β-strand	423-430	8	3
β-strand	436-446	11	3
α-helix	453-455	3
β-strand	456-463	8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endothelial PAS domain-containing protein 1	A	protein	115	Homo sapiens	Q99814 (AlphaFold model)
Aryl hydrocarbon receptor nuclear translocator	B	protein	117	Homo sapiens	P27540 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5TBM_1 Endothelial PAS domain-containing protein 1 (chains A)
GEFLGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSH
QNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIE

Sequence of entity 2 (B), FASTA

>5TBM_2 Aryl hydrocarbon receptor nuclear translocator (chains B)
GEFLGNVCQPTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRD
SFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNS

Ligands and cofactors

ID	Name	Formula	Copies
79A	3-{[(1S)-2,2-difluoro-1-hydroxy-7-(methylsulfonyl)-2,3-dihydro-1H-inden-4-yl]ox…	C17 H12 F3 N O4 S	1

Primary citation

A Small-Molecule Antagonist of HIF2 alpha Is Efficacious in Preclinical Models of Renal Cell Carcinoma. Wallace, E.M., Rizzi, J.P., Han, G. et al. Cancer Res (2016) 76:5491-5500. DOI 10.1158/0008-5472.CAN-16-0473 · PubMed

Other PDB entries of the same protein (UniProt Q99814 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3F1P 1.17 Å, Crystal structure of a high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS…
7Q5V 1.17 Å, Hif prolyl hydroxylase 2 (PHD2/EGLN1) in complex with N-oxalylglycine (NOG) and hif-2…
7Q5X 1.21 Å, Hif prolyl hydroxylase 2 (PHD2/EGLN1) in complex with 2-oxoglutarate (2OG) and hif-2…
8Q64 1.36 Å, Crystal structure of hydroxylated HIF2alpha-CODD peptide (523-542) bound to apo-HIF…
8Q6E 1.37 Å, Aerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with…
8RV1 1.39 Å, HIF prolyl hydroxylase 2 (PHD2) T387S variant bound to acetate (ACT) and hydroxylated…
8Q6D 1.4 Å, Anaerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with…
3F1N 1.48 Å, Crystal structure of a high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS…
8Q5S 1.49 Å, Anaerobic crystal structure of apo-HIF prolyl hydroxylase 2 (PHD2 181-407)in complex…
3H82 1.5 Å, Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS…
4GHI 1.5 Å, Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS…
6D0C 1.5 Å, Crystal structure of HIF2a-B*:ARNT-B* complex

Browse structure collections

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