satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (Y165A) (PDB entry 5D1L)
Macromolecule: Ubiquitin-conjugating enzyme E2 D2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2.19
Sequence length: 147 residues
Sequence: MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.618
R work: 0.1817
R free: 0.1995
Average B factor: 30.6192
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 292
Crystal growth procedure: 15% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Matthews coefficient: 2.33
Solvent content (%): 47.31
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2015-10-28
Crystal structure of the human Tankyrase 2 (TNKS2) SAM domain (DH902/924RE) (PDB entry 5JRT)
Macromolecule: Tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 77 residues
Sequence: SNAEKKEVPGVDFSITQFVRNLGLEHLMDIFEREQITLRVLVEMGHKELKEIGINAYGHREKLIKGVERLISGQQGL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.201
R free: 0.235
Average B factor: 46.71
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 285.15
Crystal growth procedure: PEG 3350 20%
0.1 MTris-HCl pH 8.5
0.2 M Ammonium Acetate
Matthews coefficient: 2.86
Solvent content (%): 57
Release date: 2016-08-03
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000323a (PDB entry 5QEH)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.941
R work: 0.197
R free: 0.2301
Average B factor: 39.9238
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.33
Solvent content (%): 63.02
Ligand: 4-[2-(phenylsulfanyl)ethyl]morpholine (JJG)
Ligand formula: C12 H17 N O S
Ligand molecular weight: 223.334
Ligand SMILES: c1ccc(cc1)SCCN2CCOCC2
Ligand InChI: InChI=1S/C12H17NOS/c1-2-4-12(5-3-1)15-11-8-13-6-9-14-10-7-13/h1-5H,6-11H2
Release date: 2018-10-10
Compound 20 Bound to CK2alpha (PDB entry 7ZYR)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1674
R free: 0.2094
Average B factor: 16.49
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.02
Solvent content (%): 39.15
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2022-10-12
SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, P21 Crystal Form (PDB entry 6MBJ)
Macromolecule: Actin Peptide
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 15 residues
Sequence: TLKYPIEHGIVTNWD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.1994
R free: 0.2234
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 292
Crystal growth procedure: 0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000
Matthews coefficient: 2.52
Solvent content (%): 51.1
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2018-12-19
X-ray Structure of CLK2-KD(130-496)/TG003 at 2.6A (PDB entry 6FYI)
Macromolecule: Dual specificity protein kinase CLK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 368 residues
Sequence: SMRSSSHSSRRAKSVEDDAEGHLIYHVGDWLQERYEIVSTLGEGTFGRVVQCVDHRRGGARVALKIIKNVEKYKEAARLEINVLEKINEKDPDNKNLCVQMFDWFDYHGHMCISFELLGLSTFDFLKDNNYLPYPIHQVRHMAFQLCQAVKFLHDNKLTHTDLKPENILFVNSDYELTYNLEKKRDERSVKSTAVRVVDFGSATFDHEHHSTIVSTRHYRAPEVILELGWSQPCDVWSIGCIIFEYYVGFTLFQTHDNREHLAMMERILGPIPSRMIRKTRKQKYFYRGRLDWDENTSAGRYVRENCKPLRRYLTSEAEEHHQLFDLIESMLEYEPAKRLTLGEALQHPFFARLRAEPPNKLWDSSRD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2178
R free: 0.233
Average B factor: 37.337
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG3350, 0.1M HEPES
Matthews coefficient: 2.12
Solvent content (%): 41.99
Ligand: (1~{Z})-1-(3-ethyl-5-methoxy-1,3-benzothiazol-2-ylidene)propan-2-one (EAE)
Ligand formula: C13 H15 N O2 S
Ligand molecular weight: 249.329
Ligand SMILES: CCN1c2cc(ccc2SC1=CC(=O)C)OC
Ligand InChI: InChI=1S/C13H15NO2S/c1-4-14-11-8-10(16-3)5-6-12(11)17-13(14)7-9(2)15/h5-8H,4H2,1-3H3/b13-7-
Release date: 2018-07-18
The Fk1 domain of FKBP51 in complex with (2R,5S,12R)-12-cyclohexyl-2-[2-(3,4-dimethoxyphenyl)ethyl]-15,15,16-trimethyl-3,19-dioxa-10,13,16-triazatricyclo[18.3.1.0^5,^10]tetracosa-1(24),20,22-triene-4,11,14,17-tetrone (PDB entry 7AWF)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1941
R free: 0.2434
Average B factor: 21.766
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 28% PEG3350 
0.1M HEPES pH 7.5
0.2M ammonium thiocyanate NH4 SCN
Matthews coefficient: 2.23
Solvent content (%): 44.77
Ligand: (2~{R},5~{S},12~{R})-12-cyclohexyl-2-[2-(3,4-dimethoxyphenyl)ethyl]-15,15,16-trimethyl-3,19-dioxa-10,13,16-triazatricyclo[18.3.1.0^{5,10}]tetracosa-1(24),20,22-triene-4,11,14,17-tetrone (S8N)
Ligand formula: C38 H51 N3 O8
Ligand molecular weight: 677.827
Ligand SMILES: CC1(C(=O)NC(C(=O)N2CCCCC2C(=O)OC(c3cccc(c3)OCC(=O)N1C)CCc4ccc(c(c4)OC)OC)C5CCCCC5)C
Ligand InChI: InChI=1S/C38H51N3O8/c1-38(2)37(45)39-34(26-12-7-6-8-13-26)35(43)41-21-10-9-16-29(41)36(44)49-30(19-17-25-18-20-31(46-4)32(22-25)47-5)27-14-11-15-28(23-27)48-24-33(42)40(38)3/h11,14-15,18,20,22-23,26,29-30,34H,6-10,12-13,16-17,19,21,24H2,1-5H3,(H,39,45)/t29-,30+,34+/m0/s1
Release date: 2021-04-21
Crystal structure of human GPX4-U46C in complex with LOC1886 (PDB entry 7U4M)
Macromolecule: Phospholipid hydroperoxide glutathione peroxidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.1.12
Sequence length: 192 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMLEAASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQCGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.1611
R free: 0.1971
Average B factor: 44.088
Crystallization method: MICROBATCH
Crystallization pH: 4.6
Crystallization temperature (K): 291
Crystal growth procedure: 2 M sodium chloride and 0.1 M sodium acetate trihydrate
Matthews coefficient: 2.74
Solvent content (%): 55.15
Ligand: 4-methoxy-1H-indole-2-carbaldehyde (LBI)
Ligand formula: C10 H9 N O2
Ligand molecular weight: 175.184
Ligand SMILES: COc1cccc2c1cc([nH]2)C=O
Ligand InChI: InChI=1S/C10H9NO2/c1-13-10-4-2-3-9-8(10)5-7(6-12)11-9/h2-6,11H,1H3
Release date: 2022-12-07
Crystal Structure of the Human CAMKK2B in complex with BI2526 (PDB entry 6BQQ)
Macromolecule: Calcium/calmodulin-dependent protein kinase kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 291 residues
Sequence: SMQLNQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAGFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNTVGTPAFMAPESLSETRKIFSGKALDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTRH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.19064
R free: 0.22768
Average B factor: 29.48
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 22% PEG 3350; 0.21 M Ammonium Sulphate; 0.1M CHC buffer pH 7.5
Matthews coefficient: 2.43
Solvent content (%): 49.46
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2017-12-13
Bromodomain of EP300 liganded with CCS-1477 (PDB entry 8FVF)
Macromolecule: Histone acetyltransferase p300
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 114 residues
Sequence: IFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1813
R free: 0.2389
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M Sodium chloride, 0.1M HEPES pH7.5, 1.6M Ammonium sulfate
Matthews coefficient: 2.89
Solvent content (%): 57.5
Ligand: (6S)-1-[3,4-bis(fluoranyl)phenyl]-6-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-(4-methoxycyclohexyl)benzimidazol-2-yl]piperidin-2-one (JHL)
Ligand formula: C30 H32 F2 N4 O3
Ligand molecular weight: 534.597
Ligand SMILES: Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)C5CCCC(=O)N5c6ccc(c(c6)F)F
Ligand InChI: InChI=1S/C30H32F2N4O3/c1-17-29(18(2)39-34-17)19-7-14-26-25(15-19)33-30(36(26)20-8-11-22(38-3)12-9-20)27-5-4-6-28(37)35(27)21-10-13-23(31)24(32)16-21/h7,10,13-16,20,22,27H,4-6,8-9,11-12H2,1-3H3/t20-,22-,27-/m0/s1
Release date: 2024-02-07
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000270a (PDB entry 5QEC)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.673
R work: 0.1852
R free: 0.2165
Average B factor: 38.8122
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.33
Solvent content (%): 63.1
Ligand: 4-(benzyloxy)benzoic acid (02S)
Ligand formula: C14 H12 O3
Ligand molecular weight: 228.243
Ligand SMILES: c1ccc(cc1)COc2ccc(cc2)C(=O)O
Ligand InChI: InChI=1S/C14H12O3/c15-14(16)12-6-8-13(9-7-12)17-10-11-4-2-1-3-5-11/h1-9H,10H2,(H,15,16)
Release date: 2018-10-10
ATAD2 in complex with PepLite-Gly (PDB entry 7Z9J)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1891
R free: 0.2213
Average B factor: 36.854
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
Matthews coefficient: 4.1
Solvent content (%): 69.98
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2022-11-23
Crystal structure of CDK2 in complex with 6-methoxy-7H-purine processed with the CrystalDirect automated mounting and cryo-cooling technology (PDB entry 5ANE)
Macromolecule: CYCLIN-DEPENDENT KINASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.20431
R free: 0.25178
Average B factor: 22.965
Crystal growth procedure: 0.02 M HEPES, PH=7.0, 5% GLYCEROL, 12% PEG 3350
Matthews coefficient: 1.99
Solvent content (%): 38.19
Ligand: 6-METHOXY-9H-PURINE (SZL)
Ligand formula: C6 H6 N4 O
Ligand molecular weight: 150.138
Ligand SMILES: COc1c2c([nH]cn2)ncn1
Ligand InChI: InChI=1S/C6H6N4O/c1-11-6-4-5(8-2-7-4)9-3-10-6/h2-3H,1H3,(H,7,8,9,10)
Release date: 2016-04-13
Crystal structure of EGFR_wt in complex with covalently bound fragment 4 (PDB entry 8HV2)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSPSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.17741
R free: 0.21645
Average B factor: 80.348
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 292
Crystal growth procedure: 0.1M TRIS pH 7.0, 1.2M Sodium citrate
Matthews coefficient: 3.41
Solvent content (%): 63.9
Ligand: ~{N}-pyridin-2-ylprop-2-enamide (MWU)
Ligand formula: C8 H8 N2 O
Ligand molecular weight: 148.162
Ligand SMILES: C=CC(=O)Nc1ccccn1
Ligand InChI: InChI=1S/C8H8N2O/c1-2-8(11)10-7-5-3-4-6-9-7/h2-6H,1H2,(H,9,10,11)
Release date: 2023-12-13
Crystal structure of WNK3 kinase domain in a diphosphorylated state and in complex with AMP-PNP/Mg2+ (PDB entry 5O26)
Macromolecule: Serine/threonine-protein kinase WNK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 284 residues
Sequence: SMAEMKAVATSPSGRFLKFDIELGRGAFKTVYKGLDTETWVEVAWCELQDRKLTKAEQQRFKEEAEMLKGLQHPNIVRFYDSWESILKGKKCIVLVTELMTSGTLKTYLKRFKVMKPKVLRSWCRQILKGLQFLHTRTPPIIHRDLKCDNIFITGPTGSVKIGDLGLATLMRTSFAKSVIGTPEFMAPEMYEEHYDESVDVYAFGMCMLEMATSEYPYSECQNAAQIYRKVTSGIKPASFNKVTDPEVKEIIEGCIRQNKSERLSIRDLLNHAFFAEDTGLRVE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.379
R work: 0.2284
R free: 0.2781
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG3350, 0.1M bis-tris pH 5.5
Matthews coefficient: 2.15
Solvent content (%): 42.85
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2017-06-28
Crystal structure of hMTH1 N33G in complex with LW14 in the absence of acetate (PDB entry 6GLQ)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 182 residues
Sequence: MKHHHHHHPMSDYDIPTTENLYFQGAMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWGGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.601
R work: 0.1723
R free: 0.2101
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: crystallized in: 23-27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5

soaked in: 0.27 M ammonium sulfate, 17% glycerol, 27% PEG4000, 20% DMSO, 10 mM compound
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2019-02-20
Human PARP14 (ARTD8), catalytic fragment in complex with inhibitor ITK6 (PDB entry 6FZM)
Macromolecule: Poly [ADP-ribose] polymerase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 193 residues
Sequence: SMDMKQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.67
R work: 0.235
R free: 0.289
Average B factor: 51.93
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 20% Poly(ethylene glycol) 3350, 0.2M sodium nitrate and 0.1M Bis-Tris-Propane
Matthews coefficient: 2.35
Solvent content (%): 47.71
Ligand: 4-[(8-methyl-4-oxidanylidene-7-prop-1-ynyl-3~{H}-quinazolin-2-yl)methylsulfanyl]benzoic acid (EE5)
Ligand formula: C20 H16 N2 O3 S
Ligand molecular weight: 364.418
Ligand SMILES: CC#Cc1ccc2c(c1C)N=C(NC2=O)CSc3ccc(cc3)C(=O)O
Ligand InChI: InChI=1S/C20H16N2O3S/c1-3-4-13-7-10-16-18(12(13)2)21-17(22-19(16)23)11-26-15-8-5-14(6-9-15)20(24)25/h5-10H,11H2,1-2H3,(H,24,25)(H,21,22,23)
Release date: 2019-02-20
Human Carbonic Anhydrase II in complex with (3-((N-(4-sulfamoylbenzyl)phenylsulfonamido)methyl)phenyl)glycine (PDB entry 8QF7)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.225
R work: 0.1167
R free: 0.1524
Average B factor: 17.268
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Matthews coefficient: 2.11
Solvent content (%): 41.61
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2024-09-11
Potent and selective inhibitors of MTH1 probe its role in cancer cell survival (PDB entry 5ANT)
Macromolecule: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 175 residues
Sequence: GSSHHHHHHSSGLVPRGSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.214
R free: 0.251
Average B factor: 29.8
Matthews coefficient: 3.1
Solvent content (%): 60
Ligand: 2-(2-methoxyethoxy)-6-(methylamino)-9-(phenylmethyl)-7H-purin-8-one (RJE)
Ligand formula: C16 H19 N5 O3
Ligand molecular weight: 329.354
Ligand SMILES: CNc1c2c(nc(n1)OCCOC)N(C(=O)N2)Cc3ccccc3
Ligand InChI: InChI=1S/C16H19N5O3/c1-17-13-12-14(20-15(19-13)24-9-8-23-2)21(16(22)18-12)10-11-6-4-3-5-7-11/h3-7H,8-10H2,1-2H3,(H,18,22)(H,17,19,20)
Release date: 2016-03-02
Crystal structure of SmyD3 in complex with covalent inhibitor 4 (PDB entry 5YJO)
Macromolecule: Histone-lysine N-methyltransferase SMYD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 423 residues
Sequence: PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.135
R work: 0.1901
R free: 0.2317
Average B factor: 24.2532
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.2M Magnesium acetate, 17% PEG3350
Matthews coefficient: 2.25
Solvent content (%): 45.36
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2018-10-17