satarupa22/MacromolecularLigandDB huggingface dataset:
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000527a (PDB entry 7GT3)
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): 1.59
R work: 0.1985
R free: 0.2295
Average B factor: 33.883
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.31
Solvent content (%): 62.84
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
selenol bound carbonic anhydrase I (PDB entry 6SWM)
Macromolecule: Carbonic anhydrase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 261 residues
Sequence: MASPDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.77
R work: 0.2723
R free: 0.3295
Average B factor: 46.333
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 296
Crystal growth procedure: 28-31% PEG4000, 0.2 M Sodium acetate, 0.1 M Tris pH 8.5-9.0
Matthews coefficient: 2.29
Solvent content (%): 46.33
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: 2020-10-07
Crystal structure of HIPK2 in complex with MU135 (compound 21e) (PDB entry 7NCF)
Macromolecule: Homeodomain-interacting protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 367 residues
Sequence: SMDYQLVQHEVLCSMTNTYEVLEFLGRGTFGQVVKCWKRGTNEIVAIKILKNHPSYARQGQIEVSILARLSTESADDYNFVRAYECFQHKNHTCLVFEMLEQNLYDFLKQNKFSPLPLKYIRPVLQQVATALMKLKSLGLIHADLKPENIMLVDPSRQPYRVKVIDFGSASHVSKAVCSTYLQSRYYRAPEIILGLPFCEAIDMWSLGCVIAELFLGWPLYPGASEYDQIRYISQTQGLPAEYLLSAGTKTTRFFNRDTDSPYPLWRLKTPDDHEAETGIKSKEARKYIFNCLDDMAQVNMTTDLEGSDMLVEKADRREFIDLLKKMLTIDADKRITPIETLNHPFVTMTHLLDFPHSTHVKSCFQN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.72
R work: 0.1948
R free: 0.2514
Average B factor: 89.316
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 10% v/v isopropanol, 0.2 M NaCl and 0.1 M HEPES, pH 7.5
Matthews coefficient: 3.46
Solvent content (%): 64.44
Ligand: 3-(4-Tert-butylphenyl)-5-(1H-pyrazol-4-yl)furo[3,2-b]pyridine (U82)
Ligand formula: C20 H19 N3 O
Ligand molecular weight: 317.384
Ligand SMILES: CC(C)(C)c1ccc(cc1)c2coc3c2nc(cc3)c4c[nH]nc4
Ligand InChI: InChI=1S/C20H19N3O/c1-20(2,3)15-6-4-13(5-7-15)16-12-24-18-9-8-17(23-19(16)18)14-10-21-22-11-14/h4-12H,1-3H3,(H,21,22)
Release date: 2021-03-03
BACE crystal structure with bicyclic aminothiazine fragment (PDB entry 4ZSM)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 442 residues
Sequence: MAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.22677
R free: 0.25761
Average B factor: 33.165
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: PEG8000, SODIUM CACODYLATE, AMMONIUM SULFATE
Matthews coefficient: 2.69
Solvent content (%): 54.35
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: 2015-06-10
4-(2-(3-(4-iodophenyl)selenoureido)ethyl)benzenesulfonamide in complex with Carbonic Anhydrase II (PDB entry 7BHH)
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): 1.4
R work: 0.1504
R free: 0.1701
Average B factor: 17.6
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5-1.7 M sodium citrate, 0.1 M Tris pH 8.0
Matthews coefficient: 2.09
Solvent content (%): 41.1
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: 2022-03-02
Carbonic anhydrase 2 in complex with 2-chloro-5'-O-sulfamoyladenosine (PDB entry 6C7X)
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): 1.5
R work: 0.15368
R free: 0.18757
Average B factor: 14.567
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 281
Crystal growth procedure: Protein was at 10 mg/mL and was set up in 250 plus 250 nL drops with a reservoir of 50 mM Tris pH 8.0, 2.8 M ammonium sulfate at 8C
Matthews coefficient: 2.1
Solvent content (%): 41.37
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: 2018-05-23
Crystal structure of the WDR domain of human DCAF1 in complex with OICR-40155 compound (PDB entry 9BHR)
Macromolecule: DDB1- and CUL4-associated factor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 315 residues
Sequence: GASAFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62
R work: 0.14789
R free: 0.18727
Average B factor: 20.418
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG3350, 0.2 M Magnesium formate
Matthews coefficient: 2.19
Solvent content (%): 43.73
Ligand: (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{(1E)-3-[(2-methoxyethyl)amino]-3-oxoprop-1-en-1-yl}-1H-pyrrole-3-carboxamide (A1API)
Ligand formula: C26 H24 Cl2 F2 N4 O4
Ligand molecular weight: 565.396
Ligand SMILES: COCCNC(=O)C=Cc1c(c(c[nH]1)C(=O)NC(CC(=O)N)c2ccc(c(c2)Cl)F)c3ccc(cc3F)Cl
Ligand InChI: InChI=1S/C26H24Cl2F2N4O4/c1-38-9-8-32-24(36)7-6-21-25(16-4-3-15(27)11-20(16)30)17(13-33-21)26(37)34-22(12-23(31)35)14-2-5-19(29)18(28)10-14/h2-7,10-11,13,22,33H,8-9,12H2,1H3,(H2,31,35)(H,32,36)(H,34,37)/b7-6+/t22-/m0/s1
Release date: 2024-05-08
JAK2 JH2 in complex with JAK146 (PDB entry 6OAV)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.939
R work: 0.2001
R free: 0.236
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1M TRIS, PH 8.0 0.2M SODIUM ACETATE, 0.001 M TCEP, 12-24% PEG 4,000
Matthews coefficient: 2.31
Solvent content (%): 46.85
Ligand: 5-amino-3-[(4-cyanophenyl)amino]-N-phenyl-1H-1,2,4-triazole-1-carboxamide (M3A)
Ligand formula: C16 H13 N7 O
Ligand molecular weight: 319.321
Ligand SMILES: c1ccc(cc1)NC(=O)n2c(nc(n2)Nc3ccc(cc3)C#N)N
Ligand InChI: InChI=1S/C16H13N7O/c17-10-11-6-8-13(9-7-11)19-15-21-14(18)23(22-15)16(24)20-12-4-2-1-3-5-12/h1-9H,(H,20,24)(H3,18,19,21,22)
Release date: 2020-03-25
HUMANISED MONOMERIC RADA IN COMPLEX WITH FHTU TETRAPEPTIDE (PDB entry 5FOT)
Macromolecule: DNA REPAIR AND RECOMBINATION PROTEIN RADA
Type: Protein, polypeptide(L)
Source organism: Pyrococcus furiosus
EC number: 3.6.4
Sequence length: 231 residues
Sequence: MATIGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVMWIDTENTFRPERIREIAQNRGLDPDEVLKHIAYARAFNSNHQMLLVQQAEDMIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQVQANGGHILAHSATLRVYLRKGKGGKRIARLIDAPHLPEGEAVFSITEKGIED
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.189
R work: 0.1324
R free: 0.1567
Average B factor: 14.6
Crystallization pH: 6.2
Crystal growth procedure: 8% PEG-1000, 100 MM NAK PHOSPHATE, PH 6.2
Matthews coefficient: 2.11
Solvent content (%): 41.4
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2016-03-30
Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence derived from S. cerevisiae BDF2 gene (PDB entry 5ED1)
Macromolecule: Double-stranded RNA-specific editase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4.37
Sequence length: 403 residues
Sequence: LHLDQTPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGQGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLTP
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.77
R work: 0.1627
R free: 0.2234
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M MES/NaOH, pH 6.5, 9% w/v PEG3350, 13% glycerol, 0.015 M NAD
Matthews coefficient: 2.44
Solvent content (%): 55.1
Ligand: INOSITOL HEXAKISPHOSPHATE (IHP)
Ligand formula: C6 H18 O24 P6
Ligand molecular weight: 660.035
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C6H18O24P6/c7-31(8,9)25-1-2(26-32(10,11)12)4(28-34(16,17)18)6(30-36(22,23)24)5(29-35(19,20)21)3(1)27-33(13,14)15/h1-6H,(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3-,4+,5-,6-
Release date: 2016-04-13
Structure of human galactokinase 1 bound with 2-(4-chlorophenyl)-N-(pyrimidin-2-yl)acetamide (PDB entry 6ZGV)
Macromolecule: Galactokinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.6
Sequence length: 399 residues
Sequence: MAHHHHHHAALRQPQVAELLAEARRAFREEFGAEPELAVSAPGRVNLIGEHTDYNQGLVLPMALELMTVLVGSPRKDGLVSLLTTSEGADEPQRLQFPLPTAQRSLEPGTPRWANYVKGVIQYYPAAPLPGFSAVVVSSVPLGGGLSSSASLEVATYTFLQQLCPDSGTIAARAQVCQQAEHSFAGMPCGIMDQFISLMGQKGHALLIDCRSLETSLVPLSDPKLAVLITNSNVRHSLASSEYPVRRRQCEEVARALGAASLREVQLEELEAARDLVSKEGFRRARHVVGEIRRTAQAAAALRRGDYRAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMTGGGFGGCTVTLLEASAAPHAMRHIQEHYGGTATFYLSQAADGAKVLCL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2069
R free: 0.2458
Average B factor: 45.848
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MOPS/sodium HEPES pH 7.0-7.5, 40-50 % Morpheus Precipitant Mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1 M Morpheus Carboxylic acids mix (0.02M each of:sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate and sodium oxamate).
Matthews coefficient: 2.97
Solvent content (%): 58.54
Ligand: beta-D-galactopyranose (GAL)
Ligand formula: C6 H12 O6
Ligand molecular weight: 180.156
Ligand SMILES: C(C1C(C(C(C(O1)O)O)O)O)O
Ligand InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4+,5-,6-/m1/s1
Release date: 2020-07-29
Crystal structure of di-phosphorylated human CLK1 in complex with 4-(1H-indol-3-yl)pyrimidin-2-amine (PDB entry 7O9Y)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 337 residues
Sequence: HLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRRCKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.21709
R free: 0.24626
Average B factor: 36.683
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG3350, 200mM MgCl2, 100mM BisTris (pH 6.5)
Matthews coefficient: 2.45
Solvent content (%): 49.8
Ligand: 4-(1~{H}-indol-3-yl)pyrimidin-2-amine (V5T)
Ligand formula: C12 H10 N4
Ligand molecular weight: 210.235
Ligand SMILES: c1ccc2c(c1)c(c[nH]2)c3ccnc(n3)N
Ligand InChI: InChI=1S/C12H10N4/c13-12-14-6-5-11(16-12)9-7-15-10-4-2-1-3-8(9)10/h1-7,15H,(H2,13,14,16)
Release date: 2022-05-04
Crystal structure of human AMPK heterotrimer in complex with allosteric activator C455 (PDB entry 8BIK)
Macromolecule: 5'-AMP-activated protein kinase catalytic subunit alpha-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 559 residues
Sequence: MHHHHHHMAEKQKHDGRVKIGHYVLGDTLGVGTFGKVKIGEHQLTGHKVAVKILNRQKIRSLDVVGKIKREIQNLKLFRHPHIIKLYQVISTPTDFFMVMEYVSGGELFDYICKHGRVEEMEARRLFQQILSAVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSCGVILYALLCGTLPFDDEHVPTLFKKIRGGVFYIPEYLNRSVATLLMHMLQVDPLKRATIKDIREHEWFKQDLPSYLFPEDPSYDANVIDDEAVKEVCEKFECTESEVMNSLYSGDPQDQLAVAYHLIIDNRRIMNQASEFYLASSPPSGSFMDDSAMHIPPGLKPHPERMPPLIADSPKARCPLDALNTTKPKSLAVKKAKWHLGIRSQSKPYDIMAEVYRAMKQLDFEWKVVNAYHLRVRRKNPVTGNYVKMSLQLYLVDNRSYLLDFKSIDDEVVEQRSGSSTPQRSCSAAGLHRPRSSFDSTTAESHSLSGSLTGSLTGSTLSSVSPRLGSHTMDFFEMCASLITTLAR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.181
R free: 0.215
Average B factor: 67.72
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: AMPK a2b1g1 (5 mg/ml: 38 uM) was combined with AMP (4-fold excess), staurosporine (1.2-fold excess) and activator 455 (3-fold excess): and crystallised at 20 C by mixing 2 ul of the protein solution with 1 ul of 8 % PEG3350, 0.3 M guanidine hydrochloride, 0.1 M PIPES buffer pH 7.2.
Matthews coefficient: 2.55
Solvent content (%): 51.72
Ligand: STAUROSPORINE (STU)
Ligand formula: C28 H26 N4 O3
Ligand molecular weight: 466.531
Ligand SMILES: CC12C(C(CC(O1)n3c4ccccc4c5c3c6n2c7ccccc7c6c8c5C(=O)NC8)NC)OC
Ligand InChI: InChI=1S/C28H26N4O3/c1-28-26(34-3)17(29-2)12-20(35-28)31-18-10-6-4-8-14(18)22-23-16(13-30-27(23)33)21-15-9-5-7-11-19(15)32(28)25(21)24(22)31/h4-11,17,20,26,29H,12-13H2,1-3H3,(H,30,33)/t17-,20-,26-,28+/m1/s1
Release date: 2024-05-15
Human PrimPol extending from the correct primer base C opposite the 8-oxoguanine lesion (PDB entry 7JL8)
Macromolecule: DNA-directed primase/polymerase protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7
Sequence length: 354 residues
Sequence: MNRKWEAKLKQIEERASHYERKPLSSVYRPRLSKPEEPPSIWRLFHRQAQAFNFVKSCKEDVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKPANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFKDNIHVGNFLRKILQPALDLLGSEDDDSAPETTGHGFPHFSEAPARQGFSFNKMFTEKATEESWTSNSKKLERLGSAEQSSPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGKRVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEPSQNKQK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1871
R free: 0.2133
Average B factor: 65.1446
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 225-250 mM CaCl2, 16-19% PEG 3350
Matthews coefficient: 2.2
Solvent content (%): 44.15
Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTP)
Ligand formula: C10 H16 N5 O12 P3
Ligand molecular weight: 491.182
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
Release date: 2021-06-30
HUMAN PI4KIIIB IN COMPLEX WITH COVALENTLY BOUND INHIBITOR (COMPOUND 11) (PDB entry 8Q6H)
Macromolecule: Phosphatidylinositol 4-kinase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.67
Sequence length: 424 residues
Sequence: GRTASNPKVENEDEPVRLAPEREFIKSLMAIGKRLATLPTKEQKTQRLISELSLLNHKLPARVWLPTAGFDHHVVRVPHTQAVVLNSKDKAPYLIYVEVLECENFDTTSVPARIPENRIQSTQSVETAFKRDPEDPSAVALKEPWQEKVRRIREGSPYGHLPNWRLLSVIVKCGDDLRQELLAFQVLKQLQSIWEQERVPLWIKPYKILVISADSGMIEPVVNAVSIHQVKKQSQLSLLDYFLQEHGSYTTEAFLSAQRNFVQSCAGYCLVCYLLQVKDRHNGNILLDAEGHIIHIDFGFILSSSPRNLGFETSAFKLTTEFVDVMGGLDGDMFNYYKMLMLQGLIAARKHMDKVVQIVEIMQQGSQLPCFHGSSTIRNLKERFHMSMTEEQLQLLVEQMVDGSMRSITTKLYDGFQYLTNGIM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.16952
R free: 0.23679
Average B factor: 32.21
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: Sodium Formate
Matthews coefficient: 2.21
Solvent content (%): 44.26
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2023-12-13
Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with acarbose (PDB entry 5NN8)
Macromolecule: Lysosomal alpha-glucosidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.20
Sequence length: 872 residues
Sequence: QCDVPPNSRFDCAPDKAITQEQCEARGCCYIPAKQGLQGAQMGQPWCFFPPSYPSYKLENLSSSEMGYTATLTRTTPTFFPKDILTLRLDVMMETENRLHFTIKDPANRRYEVPLETPRVHSRAPSPLYSVEFSEEPFGVIVHRQLDGRVLLNTTVAPLFFADQFLQLSTSLPSQYITGLAEHLSPLMLSTSWTRITLWNRDLAPTPGANLYGSHPFYLALEDGGSAHGVFLLNSNAMDVVLQPSPALSWRSTGGILDVYIFLGPEPKSVVQQYLDVVGYPFMPPYWGLGFHLCRWGYSSTAITRQVVENMTRAHFPLDVQWNDLDYMDSRRDFTFNKDGFRDFPAMVQELHQGGRRYMMIVDPAISSSGPAGSYRPYDEGLRRGVFITNETGQPLIGKVWPGSTAFPDFTNPTALAWWEDMVAEFHDQVPFDGMWIDMNEPSNFIRGSEDGCPNNELENPPYVPGVVGGTLQAATICASSHQFLSTHYNLHNLYGLTEAIASHRALVKARGTRPFVISRSTFAGHGRYAGHWTGDVWSSWEQLASSVPEILQFNLLGVPLVGADVCGFLGNTSEELCVRWTQLGAFYPFMRNHNSLLSLPQEPYSFSEPAQQAMRKALTLRYALLPHLYTLFHQAHVAGETVARPLFLEFPKDSSTWTVDHQLLWGEALLITPVLQAGKAEVTGYFPLGTWYDLQTVPIEALGSLPPPPAAPREPAIHSEGQWVTLPAPLDTINVHLRAGYIIPLQGPGLTTTESRQQPMALAVALTKGGEARGELFWDDGESLEVLERGAYTQVIFLARNNTIVNELVRVTSEGAGLQLQKVTVLGVATAPQQVLSNGVPVSNFTYSPDTKVLDICVSLLMGEQFLVSWC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.17422
R free: 0.21231
Average B factor: 30.355
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 1.9 M ammonium sulphate, 0.1 M HEPES pH 7.0, 2% v/v PEG400
Matthews coefficient: 3.39
Solvent content (%): 63.73
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: 2017-10-25
Dcps in complex with covalent inhibitor (PDB entry 4QDE)
Macromolecule: m7GpppX diphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.59
Sequence length: 337 residues
Sequence: GADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2088
R free: 0.2514
Average B factor: 65.73
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4
Crystallization temperature (K): 293
Crystal growth procedure: 1:1 protein (4 mg/mL in 25 mM sodium chloride, 20 mM Tris-HCl, pH 8.0, 1 mM TCEP) to precipitant (23-25% PEG3350, 0.1 M potassium phosphate monobasic, 0.05 M sodium chloride, 26% glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 2.35
Solvent content (%): 47.62
Ligand: 2-{[(2,4-diaminoquinazolin-5-yl)oxy]methyl}benzenesulfonic acid (30S)
Ligand formula: C15 H14 N4 O4 S
Ligand molecular weight: 346.361
Ligand SMILES: c1ccc(c(c1)COc2cccc3c2c(nc(n3)N)N)S(=O)(=O)O
Ligand InChI: InChI=1S/C15H14N4O4S/c16-14-13-10(18-15(17)19-14)5-3-6-11(13)23-8-9-4-1-2-7-12(9)24(20,21)22/h1-7H,8H2,(H,20,21,22)(H4,16,17,18,19)
Release date: 2015-05-13