Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Fragment Screening and Structure-Guided Development of Heparanase Inhibitors Reveal Orthosteric and Allosteric Inhibition
Journal, issue, pages	Acs Med. Chem. Lett., Year 2026
Publish date	Apr 3, 2025 (structure data deposition date)
Authors	Davies, L.J. / Whitefield, C. / Kim, H. / Nitsche, C. / Jackson, C.J. / Frkic, R.L.
External links	Acs Med. Chem. Lett. / Search PubMed
Methods	X-ray diffraction
Resolution	1.65 - 2.6 Å
Structure data	PDB-9o1r: Heparanase P6 in complex with fragment J4 Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-9o1s: Heparanase P6 in complex with fragment J11 Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-9o1t: Heparanase P6 in complex with fragment J13 Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-9o1u: Heparanase P6 in complex with fragment J16 Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-9o1v: Heparanase P6 in complex with fragment J21 Method: X-RAY DIFFRACTION / Resolution: 2.05 Å PDB-9o1w: Heparanase P6 in complex with fragment J25 Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-9o1x: Heparanase P6 in complex with fragment J28 Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-9o1y: Heparanase P6 in complex with fragment J29 Method: X-RAY DIFFRACTION / Resolution: 2 Å PDB-9o1z: Heparanase P6 in complex with fragment J31 Method: X-RAY DIFFRACTION / Resolution: 2.5 Å PDB-9o20: Heparanase P6 in complex with fragment J32 Method: X-RAY DIFFRACTION / Resolution: 1.83 Å PDB-9o21: Heparanase P6 in complex with fragment J34 Method: X-RAY DIFFRACTION / Resolution: 1.82 Å PDB-9o22: Heparanase P6 in complex with fragment J36 Method: X-RAY DIFFRACTION / Resolution: 2.1 Å PDB-9o23: Heparanase P6 in complex with fragment J37 Method: X-RAY DIFFRACTION / Resolution: 2.2 Å PDB-9o24: Heparanase P6 in complex with fragment J40 Method: X-RAY DIFFRACTION / Resolution: 2.6 Å PDB-9o25: Heparanase P6 in complex with fragment J41 Method: X-RAY DIFFRACTION / Resolution: 1.65 Å PDB-9o26: Heparanase P6 in complex with fragment J51 Method: X-RAY DIFFRACTION / Resolution: 2.35 Å PDB-9o27: Heparanase P6 in complex with fragment J56 Method: X-RAY DIFFRACTION / Resolution: 2.1 Å PDB-9o28: Heparanase P6 in complex with fragment J59 Method: X-RAY DIFFRACTION / Resolution: 1.81 Å PDB-9o29: Heparanase P6 in complex with fragment J61 Method: X-RAY DIFFRACTION / Resolution: 2.2 Å PDB-9o2a: Heparanase P6 in complex with fragment J69 Method: X-RAY DIFFRACTION / Resolution: 2.1 Å PDB-9o2b: Heparanase P6 in complex with fragment J71 (caffeine) Method: X-RAY DIFFRACTION / Resolution: 2.2 Å PDB-9o2c: Heparanase P6 in complex with fragment J72 Method: X-RAY DIFFRACTION / Resolution: 1.7 Å PDB-9o2d: Heparanase P6 in complex with fragment J74 (L-norepinephrine) Method: X-RAY DIFFRACTION / Resolution: 2.3 Å PDB-9o2e: Heparanase P6 in complex with fragment J82 Method: X-RAY DIFFRACTION / Resolution: 2.1 Å PDB-9o2f: Heparanase P6 in complex with fragment J85 Method: X-RAY DIFFRACTION / Resolution: 2.5 Å PDB-9o2g: Heparanase P6 in complex with fragment J91 Method: X-RAY DIFFRACTION / Resolution: 2.28 Å PDB-9o2h: Heparanase P6 in complex with fragment J92 Method: X-RAY DIFFRACTION / Resolution: 1.75 Å PDB-9o2i: Heparanase P6 in complex with fragment C2 Method: X-RAY DIFFRACTION / Resolution: 2.5 Å PDB-9o2j: Heparanase P6 in complex with fragment C5 Method: X-RAY DIFFRACTION / Resolution: 2.15 Å PDB-9o2k: Heparanase P6 in complex with fragment C12 Method: X-RAY DIFFRACTION / Resolution: 1.73 Å PDB-9o2l: Heparanase P6 in complex with fragment C17 Method: X-RAY DIFFRACTION / Resolution: 1.9 Å PDB-9o2m: Heparanase P6 in complex with fragment C5A Method: X-RAY DIFFRACTION / Resolution: 2 Å
Chemicals	ChemComp-ACT: ACETATE ION ChemComp-PEG: DI(HYDROXYETHYL)ETHER ChemComp-EDO: 1,2-ETHANEDIOL ChemComp-46S: 1-(6-methylpyrimidin-4-yl)azepane ChemComp-SO4: SULFATE ION ChemComp-HOH: WATER ChemComp-47B: 3-(3,4-difluorophenyl)imidazo[2,1-c][1,2,4]triazine ChemComp-DMS: DIMETHYL SULFOXIDE / DMSO, precipitantYM ChemComp-47J: 1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine ChemComp, No image ChemComp-AJO: Unknown entry ChemComp-D86: [azanyl(piperidin-1-yl)methylidene]azanium ChemComp-46Y: 4,6-dimethyl-2-{[3-(morpholin-4-yl)propyl]amino}pyridine-3-carbonitrile ChemComp-PG4: TETRAETHYLENE GLYCOL / precipitantYM ChemComp-45X: 2-(pyridin-3-yl)ethanamine ChemComp-TP5: THIOPHENE-3-CARBOXIMIDAMIDE ChemComp-46H: (3S)-piperidin-3-yl(piperidin-1-yl)methanone ChemComp-8G2: (4-methoxycarbonylphenyl)methylazanium PDB-1b72: PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX ChemComp-4AV: 1-(2-chloro-5-nitrophenyl)-N-methylmethanamine ChemComp-4AS: N-methyl-1-(1-methyl-1H-imidazol-2-yl)methanamine ChemComp-47P: 2-({[(1S)-1-cyclopropylethyl](methyl)amino}methyl)quinazolin-4(3H)-one ChemComp-46L: 6-(dimethylamino)pyridine-3-carboxylic acid ChemComp-47Y: 3-[(4E)-4-imino-5,6-dimethylfuro[2,3-d]pyrimidin-3(4H)-yl]-N,N-dimethylpropan-1-amine ChemComp-8KB: (6~{R})-1,4-oxazepan-6-ol ChemComp-L3Q: (8~{a}~{S})-1,5,6,7,8,8~{a}-hexahydro-[1,3]oxazolo[3,4-a]pyrazin-3-one ChemComp-NCA: NICOTINAMIDE / medicationYM ChemComp-IJZ: 5-amino-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid ChemComp-CFF: CAFFEINE / medicationYM ChemComp-GGB: L-CANAVANINE ChemComp-LNR: L-NOREPINEPHRINE / neurotransmitter, hormoneYM ChemComp-4NC: 4-NITROCATECHOL ChemComp-3AB: 3-aminobenzamide ChemComp-N7P: 1-ACETYL-L-PROLINE ChemComp-DNC: 3,5-DINITROCATECHOL ChemComp, No image ChemComp-AUM: Unknown entry ChemComp, No image ChemComp-AII: Unknown entry ChemComp-NVU: 2-(1,2-benzoxazol-3-yl)ethanoic acid ChemComp, No image ChemComp-AQF: Unknown entry ChemComp-4F8*: 2-PHENYL-1H-IMIDAZOLE-4,5-DICARBOXYLIC ACID
Source	homo sapiens (human)
Keywords	HYDROLASE / Heparanase / small molecule / cancer / complex / therapeutics