5C5R: Human tankyrase-2

Crystal structure of human tankyrase-2 in complex with a pyranopyridone inhibitor. Determined by X-ray diffraction at 1.55 Å resolution. Released 12 Aug 2015.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,966
Mol. weight: 55.59 kDa
Ligands: ZN, 0E1
Released: 12 Aug 2015

Explore 5C5R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C5R contains 20 α-helices and 22 β-strands across 4 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	954-957	4	1
α-helix	958-959	2
α-helix	963-974	12
β-strand	992-1001	10	1
α-helix	1003-1019	17
β-strand	1026-1031	6	1
α-helix	1036-1042	7
α-helix	1046-1048	3
β-strand	1050	1	2
β-strand	1058	1	2
β-strand	1059-1062	4	1
α-helix	1065-1069	5
α-helix	1075-1077	3
β-strand	1094-1102	9	1
β-strand	1106-1111	6	1

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	954-957	4	3
α-helix	958-959	2
α-helix	963-974	12
β-strand	992-1001	10	3
α-helix	1003-1018	16
β-strand	1026-1031	6	3
α-helix	1036-1042	7
α-helix	1046-1048	3
β-strand	1050	1	4
β-strand	1058	1	4
β-strand	1059-1062	4	3
α-helix	1065-1069	5
α-helix	1075-1077	3
β-strand	1094-1102	9	3
β-strand	1106-1110	5	3

Chain C: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1118-1119	2
β-strand	1124-1129	6	1
β-strand	1138-1141	4	1
α-helix	1144-1146	3
β-strand	1147-1157	11	1

Chain D: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1117-1119	3
β-strand	1124-1128	5	3
α-helix	1135-1137	3
β-strand	1138-1141	4	3
α-helix	1144-1146	3
β-strand	1147-1157	11	3
α-helix	1158-1160	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tankyrase-2	A, B	protein	191	Homo sapiens	Q9H2K2 (AlphaFold model)
Tankyrase-2	C, D	protein	49	Homo sapiens	Q9H2K2 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5C5R_1 Tankyrase-2 (chains A, B)
MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDG
GHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHK
GFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVT
LGKSFLQFSAM

Sequence of entity 2 (C, D), FASTA

>5C5R_2 Tankyrase-2 (chains C, D)
KMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
0E1	(7R)-2-hydroxy-7-(propan-2-yl)-7,8-dihydro-5H-pyrano[4,3-b]pyridine-3-carbonitr…	C12 H14 N2 O2	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Fragment-Based Drug Design of Novel Pyranopyridones as Cell Active and Orally Bioavailable Tankyrase Inhibitors. de Vicente, J., Tivitmahaisoon, P., Berry, P. et al. ACS Med Chem Lett (2015) 6:1019-1024. DOI 10.1021/acsmedchemlett.5b00251 · PubMed

Other PDB entries of the same protein (UniProt Q9H2K2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5BXO 1.33 Å, Human Tankyrase-2 in Complex with Macrocyclised Extended Peptide cp4n2m3
5BXU 1.35 Å, Human Tankyrase-2 in Complex with Macrocyclised Extended Peptide cp4n4m5
5NWG 1.4 Å, Crystal structure of TNKS2 in complex with 7-chloro-2-{4-[(2-hydroxyethyl)(methyl)amino]p…
5NWD 1.45 Å, Crystal structure of TNKS2 in complex with 2-[4-(diethylamino)phenyl]-3,4-dihydroquinazol…
4PNL 1.5 Å, Crystal structure of TNKS-2 in complex with DR2313.
5NVE 1.5 Å, Crystal structure of TNKS2 in complex with 2-(4-ethoxyphenyl)-3,4-dihydroquinazolin-4-one
5NWC 1.5 Å, Crystal structure of TNKS2 in complex with 2-(2-aminophenyl)-3,4-dihydroquinazolin-4-one
7CE4 1.5 Å, Tankyrase2 catalytic domain in complex with K-476
5JRT 1.53 Å, Crystal structure of the human Tankyrase 2 (TNKS2) SAM domain (DH902/924RE)
3TWR 1.55 Å, Crystal structure of ARC4 from human Tankyrase 2 in complex with peptide from human 3BP2
5NVF 1.55 Å, Crystal structure of TNKS2 in complex with 2-[4-(pyridin-2-yl)phenyl]-3,4-dihydroquinazol…
4TJU 1.57 Å, Crystal Structure of human Tankyrase 2 in complex with 3,4-CPQ-5-C.

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