satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the FLT3 kinase domain bound to the inhibitor FF-10101 (PDB entry 5X02)
Macromolecule: Receptor-type tyrosine-protein kinase FLT3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 347 residues
Sequence: GPGHKYKKQFRYESQLQMVQVTGSSDNEYFYVDFREYEYDLKWEFPRENLEFGKVLGSGAFGKVMNATAYGISKTGVSIQVAVKMLKEKADSSEREALMSELKMMTQLGSHENIVNLLGACTLSGPIYLIFEYCCYGDLLNYLRSKREKFSEDEIEYENQKRLEEEEDLNVLTFEDLLCFAYQVAKGMEFLEFKSCVHRDLAARNVLVTHGKVVKICDFGLARDIMSDSNYVVRGNARLPVKWMAPESLFEGIYTIKSDVWSYGILLWEIFSLGVNPYPGIPVDANFYKLIQNGFKMDQPFYATEEIYIIMQSCWAFDSRKRPSFPNLTSFLGCQLADAEEAMYQNV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.401
R work: 0.234
R free: 0.2766
Average B factor: 74.3646
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.7
Crystallization temperature (K): 293
Crystal growth procedure: 2.2-2.4M Na/K Phosphate, 0.1M CAPS (pH6.7), 0.2M Litium Sulfate
Matthews coefficient: 3.02
Solvent content (%): 59.21
Ligand: N-[(2S)-1-[5-[2-[(4-cyanophenyl)amino]-4-(propylamino)pyrimidin-5-yl]pent-4-ynylamino]-1-oxidanylidene-propan-2-yl]-4-(dimethylamino)-N-methyl-but-2-enamide (F6M)
Ligand formula: C29 H38 N8 O2
Ligand molecular weight: 530.664
Ligand SMILES: CCCNc1c(cnc(n1)Nc2ccc(cc2)C#N)C#CCCCNC(=O)C(C)N(C)C(=O)C=CCN(C)C
Ligand InChI: InChI=1S/C29H38N8O2/c1-6-17-31-27-24(21-33-29(35-27)34-25-15-13-23(20-30)14-16-25)11-8-7-9-18-32-28(39)22(2)37(5)26(38)12-10-19-36(3)4/h10,12-16,21-22H,6-7,9,17-19H2,1-5H3,(H,32,39)(H2,31,33,34,35)/b12-10+/t22-/m0/s1
Release date: 2018-01-24
BRM (SMARCA2) Bromodomain in complex with ligand 10 (PDB entry 8QJT)
Macromolecule: Probable global transcription activator SNF2L2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4
Sequence length: 123 residues
Sequence: SMAEKLSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQKIAKEEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.568
R work: 0.2025
R free: 0.263
Average B factor: 58.14
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 6K, 6% ethylene glycol, 10 mM ZnCl2
Matthews coefficient: 2.06
Solvent content (%): 40.22
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: 2024-01-17
Crystal structure of c-Met in complex with (S)-5-(8-fluoro-3-(1-(3-(2-methoxyethoxy)quinolin-6-yl)ethyl)-[1,2,4]triazolo[4,3-a]pyridin-6-yl)-3-methylisoxazole (PDB entry 4XYF)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: QNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1858
R free: 0.2359
Average B factor: 29
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 13% PEG 4000, 100 mM HEPES, 6% (v/v) isopropanol, 3% (v/v) ethanol, 40 mM beta-mercaptoethanol
Matthews coefficient: 2.04
Solvent content (%): 39.69
Ligand: 6-{(1S)-1-[8-fluoro-6-(3-methyl-1,2-oxazol-5-yl)[1,2,4]triazolo[4,3-a]pyridin-3-yl]ethyl}-3-(2-methoxyethoxy)quinoline (44X)
Ligand formula: C24 H22 F N5 O3
Ligand molecular weight: 447.462
Ligand SMILES: Cc1cc(on1)c2cc(c3nnc(n3c2)C(C)c4ccc5c(c4)cc(cn5)OCCOC)F
Ligand InChI: InChI=1S/C24H22FN5O3/c1-14-8-22(33-29-14)18-11-20(25)24-28-27-23(30(24)13-18)15(2)16-4-5-21-17(9-16)10-19(12-26-21)32-7-6-31-3/h4-5,8-13,15H,6-7H2,1-3H3/t15-/m0/s1
Release date: 2015-03-11
CRYSTAL STRUCTURE OF HUMAN FKBP51 FK1 DOMAIN A19T MUTANT IN COMPLEX WITH 4-METHYLIMIDAZOLE (PDB entry 6TX5)
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: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.08
R work: 0.122
R free: 0.1392
Average B factor: 15.76
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 28-41% PEG3350, 0.2M NH4OAc, 0.1M HEPES
Matthews coefficient: 2.32
Solvent content (%): 46.87
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2020-05-27
The FK1 domain of FKBP51 in complex with peptide-inhibitor hit SFPFT (PDB entry 7ETU)
Macromolecule: peptide-inhibitor hit
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 5 residues
Sequence: SFPFT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.39
R work: 0.1686
R free: 0.1955
Average B factor: 10.95
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 30%-36% PEG 3350, 0.2 M Ammonium Acetate and 0.1 M HEPES pH 7.5
Matthews coefficient: 2.22
Solvent content (%): 44.54
Release date: 2022-02-23
Crystal Structure of chromodomain of CBX4 in complex with inhibitor UNC3866 (PDB entry 5EPL)
Macromolecule: E3 SUMO-protein ligase CBX4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 60 residues
Sequence: GSEHVFAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENILDPRLLIAFQNRERQEQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.183
R free: 0.216
Average B factor: 26.15
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG3350, 0.2M sodium chloride, 0.1 M sodium cacodylate
Matthews coefficient: 2.7
Solvent content (%): 53.9
Ligand: UNKNOWN ATOM OR ION (UNX)
Ligand formula: X
Ligand SMILES: *
Release date: 2015-12-23
Crystal structure of Aurora-A kinase in complex with an allosterically binding fragment (PDB entry 5OS6)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 265 residues
Sequence: QWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2124
R free: 0.2773
Average B factor: 55.1535
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Tris, pH 8.5: 0.5 M NaCl: 0.2 M MgCl2: 32.5 % v/v PEG 3350
Matthews coefficient: 2.73
Solvent content (%): 54.9
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2017-11-01
IRAK4 in complex with AZ3862 (PDB entry 5K7G)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: VSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.206
R free: 0.227
Average B factor: 47.04
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 2.5 M ammonium sulfate, 0.1 M Hepes
Matthews coefficient: 2.51
Solvent content (%): 51.07
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: 2017-12-06
Structure of the FK1 domain of the FKBP51 G64S variant 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 8BA6)
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: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNSKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.1397
R free: 0.1604
Average B factor: 12.06
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG3350 0.2M ammonium acetate 0.1 M HEPES-NaOH pH 7.5
Matthews coefficient: 2.31
Solvent content (%): 46.8
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: 2022-11-16
Human DNA Pol eta with dA-ended primer and dATP: in crystallo reaction for 100 s (PDB entry 7M80)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1569
R free: 0.2142
Average B factor: 30.6873
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: 15% PEG 2000 MME,
100 mM MES
Matthews coefficient: 2.11
Solvent content (%): 41.84
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: 2021-06-02
Structure of human MTHFD2L in complex with TH7299 (PDB entry 7QEI)
Macromolecule: Probable bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.15
Sequence length: 299 residues
Sequence: MEAIIISGTEMAKHIQKEIQRGVESWVSLGNRRPHLSIILVGDNPASHTYVRNKIRAASAVGICSELILKPKDVSQEELLDVTDQLNMDPRVSGILVQLPLPDHVDERTICNGIAPEKDVDGFHIINIGRLCLDQHSLIPATASAVWEIIKRTGIQTFGKNVVVAGRSKNVGMPIAMLLHTDGEHERPGGDATVTIAHRYTPKEQLKIHTQLADIIIVAAGIPKLITSDMVKEGAAVIDVGINYVHDPVTGKTKLVGDVDFEAVKKKAGFITPVPGGVGPMTVAMLLKNTLLAAKKIIY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.18738
R free: 0.2311
Average B factor: 21.772
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M NaF, 20 % PEG3350
Matthews coefficient: 2.06
Solvent content (%): 40.22
Ligand: (2S)-2-[[4-[[2,4-bis(azanyl)-6-oxidanylidene-1H-pyrimidin-5-yl]carbamoylamino]phenyl]carbonylamino]pentanedioic acid (9L9)
Ligand formula: C17 H19 N7 O7
Ligand molecular weight: 433.375
Ligand SMILES: c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NC(=O)NC2=C(N=C(NC2=O)N)N
Ligand InChI: InChI=1S/C17H19N7O7/c18-12-11(14(28)24-16(19)23-12)22-17(31)20-8-3-1-7(2-4-8)13(27)21-9(15(29)30)5-6-10(25)26/h1-4,9H,5-6H2,(H,21,27)(H,25,26)(H,29,30)(H2,20,22,31)(H5,18,19,23,24,28)/t9-/m0/s1
Release date: 2022-10-12
1,4-Oxazine BACE1 inhibitors (PDB entry 5CLM)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 401 residues
Sequence: ETDEEPEEPGTTGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.61
R work: 0.1902
R free: 0.25003
Average B factor: 49.026
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 12% (m/v) PEG4000, 100mM MES/NaOH pH 5.5
Matthews coefficient: 2.87
Solvent content (%): 57.11
Ligand: N-{3-[(3R)-5-amino-3-methyl-3,6-dihydro-2H-1,4-oxazin-3-yl]phenyl}-5-chloropyridine-2-carboxamide (52K)
Ligand formula: C17 H17 Cl N4 O2
Ligand molecular weight: 344.795
Ligand SMILES: CC1(COCC(=N1)N)c2cccc(c2)NC(=O)c3ccc(cn3)Cl
Ligand InChI: InChI=1S/C17H17ClN4O2/c1-17(10-24-9-15(19)22-17)11-3-2-4-13(7-11)21-16(23)14-6-5-12(18)8-20-14/h2-8H,9-10H2,1H3,(H2,19,22)(H,21,23)/t17-/m0/s1
Release date: 2015-09-30
Cyrstal structure of SKIP RUN domain in complex with GTP-bound Arl8b(Q75L) (PDB entry 8JCA)
Macromolecule: ADP-ribosylation factor-like protein 8B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 169 residues
Sequence: KEEMELTLVGLQYSGKTTFVNVIASGQFSEDMIPTVGFNMRKVTKGNVTIKIWDIGGLPRFRSMWERYCRGVNAIVYMIDAADREKIEASRNELHNLLDKPQLQGIPVLVLGNKRDLPNALDEKQLIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHSKSRRS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1746
R free: 0.206
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 800mM Potassiam phosphate dibasic
1.2 M Sodium phosphate monobasic
0.1M CAPS/Sodium hydroxide
0.2M Lithium sulfate pH10.5
Matthews coefficient: 2.5
Solvent content (%): 50.8
Ligand: GUANOSINE-5'-TRIPHOSPHATE (GTP)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2024-03-27
Crystal Structure of 1-hydroxy-4-methylpyridine-2(1H)-thione bound to human carbonic anhydrase II (PDB entry 4Q7S)
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): 1.8
R work: 0.18896
R free: 0.22616
Average B factor: 12.42
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium Sulfate, pH 8.0, VAPOR DIFFUSION, temperature 291K
Matthews coefficient: 2.08
Solvent content (%): 40.83
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: 2015-03-11
Crystal structure of human phosphodiesterase 2A with 1-(2-chloro-5-methoxy-phenyl)-N-isobutyl-4-methyl-[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide (PDB entry 6C7I)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 342 residues
Sequence: SAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.713
R work: 0.1713
R free: 0.2143
Average B factor: 28.0838
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 293
Crystal growth procedure: 17-19% PEG3350, 0.2 M magnesium chloride, 0.1 M Tris, pH 8.4
Matthews coefficient: 2.18
Solvent content (%): 43.58
Ligand: 1-(2-chloro-5-methoxyphenyl)-4-methyl-N-(2-methylpropyl)[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide (EP7)
Ligand formula: C22 H22 Cl N5 O2
Ligand molecular weight: 423.895
Ligand SMILES: Cc1c2nnc(n2c3cc(ccc3n1)C(=O)NCC(C)C)c4cc(ccc4Cl)OC
Ligand InChI: InChI=1S/C22H22ClN5O2/c1-12(2)11-24-22(29)14-5-8-18-19(9-14)28-20(13(3)25-18)26-27-21(28)16-10-15(30-4)6-7-17(16)23/h5-10,12H,11H2,1-4H3,(H,24,29)
Release date: 2018-08-15
The X-ray structure of human V216F phosphoglycerate kinase 1 mutant (PDB entry 5M3U)
Macromolecule: Phosphoglycerate kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.2.3
Sequence length: 416 residues
Sequence: SLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKFADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.192
R free: 0.24159
Average B factor: 30.912
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 2.2-2.5 M NAKPO4, PH 8.2-8.4,
Matthews coefficient: 2.02
Solvent content (%): 38.68
Ligand: 3-PHOSPHOGLYCERIC ACID (3PG)
Ligand formula: C3 H7 O7 P
Ligand molecular weight: 186.057
Ligand SMILES: C(C(C(=O)O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C3H7O7P/c4-2(3(5)6)1-10-11(7,8)9/h2,4H,1H2,(H,5,6)(H2,7,8,9)/t2-/m1/s1
Release date: 2017-12-20
PDE2 catalytic domain complexed with inhibitors (PDB entry 5U7K)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 345 residues
Sequence: GSAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.1922
R free: 0.2547
Average B factor: 36.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 25% PEG 3350, 0.1 M Tris, pH 8.5, and 0.2 M MgCl2
Matthews coefficient: 2.2
Solvent content (%): 44.14
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2017-06-28
Crystal structure of PI3K-alpha in complex with compound 30 (PDB entry 8EXU)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.137
Sequence length: 1080 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQGAMGSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVENLYFQGGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.196
R free: 0.241
Average B factor: 64.26
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.2
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MES buffer pH 6.2, 16% PEG 20,000, 0.1M KCl
Matthews coefficient: 2.19
Solvent content (%): 43.93
Ligand: (2S)-2-cyclopropyl-2-({(4S,11aM)-2-[(4S)-2-oxo-4-(trifluoromethyl)-1,3-oxazolidin-3-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepin-9-yl}amino)acetamide (X3R)
Ligand formula: C20 H20 F3 N5 O4
Ligand molecular weight: 451.399
Ligand SMILES: c1cc-2c(cc1NC(C3CC3)C(=O)N)OCCn4c2nc(c4)N5C(COC5=O)C(F)(F)F
Ligand InChI: InChI=1S/C20H20F3N5O4/c21-20(22,23)14-9-32-19(30)28(14)15-8-27-5-6-31-13-7-11(3-4-12(13)18(27)26-15)25-16(17(24)29)10-1-2-10/h3-4,7-8,10,14,16,25H,1-2,5-6,9H2,(H2,24,29)/t14-,16-/m0/s1
Release date: 2022-11-30