UniProt Q9Y251

Heparanase (Q9Y251)

Heparanase (UniProt Q9Y251), EC 3.2.1.166: 25 experimental structures and 1 predicted model on GenesisL1, 20 ligands bound, 31 pockets. Binding sites, druggability and experiment against prediction (TM-score) in GL1X.

UniProt: Q9Y251
Protein: Heparanase
EC: 3.2.1.166
Experimental structures: 25
Predicted models: 1
Ligands: 20
Pockets: 31 · 7 records with a druggable one

Structures

26 records of Q9Y251 in the MolNFT archive: 25 experimental, 1 predicted.

Entry	Title	Method	Chains	Ligands	Pockets
5E8M	Crystal structure of human heparanase	x-ray diffraction	A, B	NAG, FUC, CL	4 (best 0.53)
5E8M	Crystal structure of human heparanase	x-ray diffraction	A, B	—	—
5E97	Glycoside Hydrolase ligand structure 1	x-ray diffraction	A, B	BDP, NDG, NAG, CL, NPO	5 (best 0.55)
5E97	Glycoside hydrolase ligand structure 1	x-ray diffraction	A, B	—	—
5E98	Crystal structure of human heparanase in complex with HepMer M04S02a	x-ray diffraction	A, B	BDP, GNS, NAG, CL, NPO	—
5E98	Crystal structure of human heparanase in complex with hepmer M04S02A	x-ray diffraction	A, B	—	—
5E9B	Crystal structure of human heparanase in complex with hepmer M09S05A	x-ray diffraction	A, B	—	—
5E9C	Crystal structure of human heparanase in complex with heparin tetrasaccharide DP4	x-ray diffraction	A, B	—	—
5L9Y	Crystal structure of human heparanase, in complex with glucuronic acid configured aziridine probe…	x-ray diffraction	A, B	NAG, FUC, 6S6	—
5L9Z	Crystal structure of human heparanase nucleophile mutant (E343Q), in complex with unreacted…	x-ray diffraction	A, B	NAG, CL, GUX	—
5LA4	Crystal structure of apo human proheparanase	x-ray diffraction	A	NAG, FUC	4 (best 0.62)
5LA4	Crystal structure of apo human proheparanase	x-ray diffraction	A	NAG, FUC	—
5LA7	Crystal structure of human proheparanase, in complex with glucuronic acid configured aziridine…	x-ray diffraction	A	NAG, FUC, 6S6	—
5LA7	Crystal structure of human proheparanase, in complex with glucuronic acid configured aziridine…	x-ray diffraction	A	NAG, FUC, 6S6	—
6ZDM	Crystal structure of human heparanase in complex with a N',6O'-bis-sulfated 4-methylumbelliferyl…	x-ray diffraction	AAA, BBB	NAG, QG2, SO4	4 (best 0.57)
7PR7	Crystal structure of human heparanase in complex with covalent inhibitor VL166	x-ray diffraction	A, B	NAG, FUC, 8I4, NDG, CL	—
7PR8	Crystal structure of human heparanase in complex with covalent inhibitor GR109	x-ray diffraction	A, B	NAG, FUC, 8I4, NGY, CL	—
7PRT	Crystal structure of human heparanase in complex with covalent inhibitor CB678	x-ray diffraction	A, B	NAG, FUC, 8I4, Z61, CL	4 (best 0.49)
7PRT	Crystal structure of human heparanase in complex with covalent inhibitor CB678	x-ray diffraction	A, B	NAG, FUC, 8I4, Z61, CL	—
7RG8	Crystal Structure of a Stable Heparanase Mutant	x-ray diffraction	A, B	NA	4 (best 0.53)
7RG8	Crystal structure of a stable heparanase mutant	x-ray diffraction	A, B	NA	—
7YJC	Crystal structure of Human HPSE1 in complex with inhibitor	x-ray diffraction	A, B	IVO	—
8B0B	Crystal structure of human heparanase in complex with covalent inhibitor VB151	x-ray diffraction	AAA, BBB	NAG, OUU	—
8BAC	Crystal structure of human heparanase in complex with competitive inhibitor GD05	x-ray diffraction	AAA, BBB	NAG, SJ5	3 (best 0.54)
8CQI	Human heparanase in complex with inhibitor R3794	x-ray diffraction	A, B	NAG, VGO, LYY, CL	3 (best 0.52)
Q9Y251	AlphaFold monomer V2.0 prediction for heparanase (Q9Y251)	predicted	A	—	—

Ligands

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · in 17 records
FUC · alpha-L-fucopyranose · in 10 records
CL · Chloride ion · in 9 records
8I4 · (2R,3S,5R,6R)-2,3,4,5,6-pentakis(oxidanyl)cyclohexane-1-carboxylic acid · in 4 records
6S6 · (1~{S},2~{R},3~{S},4~{S},5~{S},6~{R})-2-(8-azidooctylamino)-3,4,5,6-tetrakis(oxidanyl) cyclohexane-1-carboxylic acid · in 3 records
BDP · beta-D-glucopyranuronic acid · in 2 records
NA · Sodium ion · in 2 records
NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · in 2 records
NPO · P-nitrophenol · in 2 records
Z61 · 2-deoxy-alpha-D-arabino-hexopyranose · in 2 records
GNS · 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose · in 1 record
GUX · (1~{R},2~{S},3~{R},4~{S},5~{S},6~{R})-7-[8-[(azanylidene-{4}-azanylidene)amino]octyl]-3,4,5-tris(oxidanyl)-7-azabicyclo[4.1.0]heptane-2-carboxylic acid · in 1 record
IVO · (5~{S},6~{R},7~{S},8~{S})-6,7,8-tris(oxidanyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid · in 1 record
LYY · 1,5-anhydro-D-arabinitol · in 1 record
NGY · 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose · in 1 record
OUU · (1~{S},2~{R},3~{R},4~{S},6~{S})-2-(2-acetamidoethoxy)-3,4,6-tris(oxidanyl)cyclohexane-1-carboxylic acid · in 1 record
QG2 · (2~{S},3~{S},4~{R},5~{R},6~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-4,5-bis(oxidanyl)-3-(sulfoamino)-6-(sulfooxymethyl)oxan-2-yl]oxy-6-(4-methyl-2-oxidanylidene-chromen-7-yl)oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid · in 1 record
SJ5 · (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid · in 1 record
SO4 · Sulfate ion · in 1 record
VGO · (3~{S},4~{S})-4,5,5-tris(oxidanyl)piperidine-3-carboxylic acid · in 1 record

Experiment against prediction

5LA4 chain A against the predicted model Q9Y251: TM-score 1.00, RMSD 0.19 Å
5LA4 chain A against the predicted model Q9Y251: TM-score 1.00, RMSD 0.19 Å
5LA7 chain A against the predicted model Q9Y251: TM-score 1.00, RMSD 0.28 Å
5LA7 chain A against the predicted model Q9Y251: TM-score 1.00, RMSD 0.28 Å
7PR8 chain A against the predicted model Q9Y251: TM-score 1.00, RMSD 0.33 Å
7PR7 chain A against the predicted model Q9Y251: TM-score 1.00, RMSD 0.34 Å
5L9Z chain A against the predicted model Q9Y251: TM-score 1.00, RMSD 0.36 Å
5E9C chain A against the predicted model Q9Y251: TM-score 1.00, RMSD 0.36 Å
5E97 chain A against the predicted model Q9Y251: TM-score 1.00, RMSD 0.37 Å
5E97 chain A against the predicted model Q9Y251: TM-score 1.00, RMSD 0.37 Å

Elsewhere

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