satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of Aurora-A kinase in complex with an allosterically binding fragment (PDB entry 5OSD)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 267 residues
Sequence: KRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.1957
R free: 0.2395
Average B factor: 54.8167
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 (%): 55.01
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
phosphodiesterase-9A in complex with inhibitor 4b (PDB entry 7F0I)
Macromolecule: Isoform PDE9A2 of High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.35
Sequence length: 533 residues
Sequence: MGSGSSSYRPKAIYLDIDGRIQKVIFSKYCNSSDIMDLFCIATGLPRNTTISLLTTDDAMVSIDPTMPANSERTPYKVRPVAIKQLSEREELIQSVLAQVAEQFSRAFKINELKAEVANHLAVLEKRVELEGLKVVEIEKCKSDIKKMREELAARSSRTNCPCKYSFLDNHKKLTPRRDVPTYPKYLLSPETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRDFSINPVTLRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKFSQTDILILMTAAICHDLDHPGYNNTYQINARTELAVRYNDISPLENHHCAVAFQILAEPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKEKMENFDYSNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQSDREKSEGLPVAPFMDRDKVTKATAQIGFIKFVLIPMFETVTKLFPMVEEIMLQPLWESRDRYEELKRIDDAMKELQKKTDSLTSGATEKSRERSRDVKNSEGDCA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.70000890032
R work: 0.270818453015
R free: 0.333696578959
Average B factor: 30.0805812221
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 3.0M Na formate, 0.1M HEPES (pH 7.5), 5% xylitol
Matthews coefficient: 2.91
Solvent content (%): 57.76
Ligand:  1-cyclopentyl-6-[[(2R)-1-(6-fluoranyl-2-azaspiro[3.3]heptan-2-yl)-1-oxidanylidene-propan-2-yl]amino]-5H-pyrazolo[3,4-d]pyrimidin-4-one (06A)
Ligand formula: C19 H25 F N6 O2
Ligand molecular weight: 388.439
Ligand SMILES: CC(C(=O)N1CC2(C1)CC(C2)F)NC3=Nc4c(cnn4C5CCCC5)C(=O)N3
Ligand InChI: InChI=1S/C19H25FN6O2/c1-11(17(28)25-9-19(10-25)6-12(20)7-19)22-18-23-15-14(16(27)24-18)8-21-26(15)13-4-2-3-5-13/h8,11-13H,2-7,9-10H2,1H3,(H2,22,23,24,27)/t11-/m1/s1
Release date: 2022-04-13
Human Carbonic anhydrases II in complex with a acetazolamide derivative comprising one hydrophobic and one hydrophilic tail moiety (PDB entry 4RN4)
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): 1.53
R work: 0.1685
R free: 0.1986
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 2.9 M ammonium sulfate with 0.1 M Tris buffer, Protein at 14 mg/mL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Matthews coefficient: 2.09
Solvent content (%): 41.07
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: 2015-01-28
Thiophenyl-Pyrazolourea Derivatives as Potent, Brian Penetrant, Orally Bioavailable, and Isoform-Selective JNK3 Inhibitors (PDB entry 7KSI)
Macromolecule: Mitogen-activated protein kinase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 464 residues
Sequence: MSLHFLYYCSEPTLDVKIAFCQGFDKQVDVSYIAKHYNMSKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNSEEKTKNGVVKGQPSPSGAAVNSSESLPPSSSVNDISSMSTDQTLASDTDSSLEASAGPLGCCR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.726
R work: 0.2195
R free: 0.2552
Average B factor: 33.77
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.2 M ammonium tartrate pH 7.0, 20 % PEG 3350
Matthews coefficient: 1.89
Solvent content (%): 34.92
Ligand: 4-(4-{[(2-chloro-6-fluorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-5-methyl-N-(oxetan-3-yl)thiophene-2-carboxamide (X3S)
Ligand formula: C19 H17 Cl F N5 O3 S
Ligand molecular weight: 449.886
Ligand SMILES: Cc1c(cc(s1)C(=O)NC2COC2)n3cc(cn3)NC(=O)Nc4c(cccc4Cl)F
Ligand InChI: InChI=1S/C19H17ClFN5O3S/c1-10-15(5-16(30-10)18(27)23-12-8-29-9-12)26-7-11(6-22-26)24-19(28)25-17-13(20)3-2-4-14(17)21/h2-7,12H,8-9H2,1H3,(H,23,27)(H2,24,25,28)
Release date: 2021-03-03
Human PP2Calpha (PPM1A) complexed with cyclic peptide c(MpSIpYVA) (PDB entry 6B67)
Macromolecule: Protein phosphatase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 296 residues
Sequence: GAFLDKPKMEKHNAQGQGNGLRYGLSSMQGWRVEMEDAHTAVIGLPSGLESWSFFAVYDGHAGSQVAKYCCEHLLDHITNNQDFKGSAGAPSVENVKNGIRTGFLEIDEHMRVMSEKKHGADRSGSTAVGVLISPQHTYFINCGESRGLLCRNRKVHFFTQDHKPSNPLEKERIQNAGGSVMIQRVNGSLAVSRALGDFDYKCVHGKGPTEQLVSPEPEVHDIERSEEDDQFIILACDGIWDVMGNEELCDFVRSRLEVTDDLEKVCNEVVDTCLYKGSRDNMSVILICFPNAPKV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.169
R free: 0.229
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 293
Crystal growth procedure: Protein conc: 20 mg/ml
Protein buffer: 10 mM MES, pH 7.0, 150 mM NaCl, 2 mM TCEP and 2 mM MgCl2
Protein and cyclic peptide was dialyzed against above buffer and mixed at the 1:2 molar ratio
Precipitant: 0.1M HEPES (pH 7.3), 0.1M calcium acetate and 40% PEG400
Matthews coefficient: 2.26
Solvent content (%): 45.55
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2018-04-11
PostInsertion complex of Human DNA Polymerase Eta bypassing an O6-Methyl-2'-deoxyguanosine : dT site (PDB entry 5L1L)
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): 1.62
R work: 0.15679
R free: 0.19348
Average B factor: 24.47
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES pH 5.5, 5mM Calcium chloride, 18% PEG 2000 MME
Matthews coefficient: 2.09
Solvent content (%): 41.22
Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine (0KX)
Ligand formula: C9 H17 N4 O12 P3
Ligand molecular weight: 466.172
Ligand SMILES: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H17N4O12P3/c10-7-1-2-13(9(15)11-7)8-3-5(14)6(24-8)4-23-26(16,17)12-27(18,19)25-28(20,21)22/h1-2,5-6,8,14H,3-4H2,(H2,10,11,15)(H2,20,21,22)(H3,12,16,17,18,19)/t5-,6+,8+/m0/s1
Release date: 2016-10-05
Carbonic Anhydrase II Inhibitor RA2 (PDB entry 5NXI)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 259 residues
Sequence: AHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.16
R work: 0.1264
R free: 0.1465
Average B factor: 15.23
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291.15
Crystal growth procedure: 50 mM Tris
1.6 M Natrium Citrate
Matthews coefficient: 2.1
Solvent content (%): 41.47
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: 2018-01-17
Crystal structure of the Burkholderia Lethal Factor 1 (BLF1) C94S inactive mutant in complex with human eIF4A - Crystal form A (PDB entry 7PPZ)
Macromolecule: Burkholderia Lethal Factor 1 (BLF1)
Type: Protein, polypeptide(L)
Source organism: Burkholderia pseudomallei K96243
Sequence length: 211 residues
Sequence: MPNSLEAQIRQAMKTGSTLTIEFDQALNQKSPGTLNVFLHPANGGVRIDLDSGNQGEPAKILWLPWKQGELQTLQPGSISTVDMLFFTYYLSGSKVFAGDGGPVWHIDAPVEANQFWRRMSSDEWMEDWEVGTDRQVAYLHRAGQSDSLWNLSAYLEGAAPSTYGRDNLGQAVVGGIVTGRQQMSLYQYATTSSGSSAWSPLTYTLQQRKQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.2016
R free: 0.2761
Average B factor: 27.593
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 290
Crystal growth procedure: 0.1 M MES, 50 mM magnesium chloride, 10 % (w/v) 2-propanol, 5 % (w/v) PEG 4000
Matthews coefficient: 2.26
Solvent content (%): 45.48
Release date: 2022-04-13
The crystal structure of hCA II in complex with a benzoxaborole inhibitor (PDB entry 5LMD)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 262 residues
Sequence: MGMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1656
R free: 0.2009
Average B factor: 14.0393
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.4 M Sodium Citrate
0.1 M Tris-HCl
Matthews coefficient: 2.13
Solvent content (%): 42.15
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: 2016-10-19
Structural basis for the binding between Tankyrase-1 and USP25 (PDB entry 5GP7)
Macromolecule: Tankyrase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 169 residues
Sequence: GPGSDLLRGDAALLDAAKKGCLARVQKLCTPENINCRDTQGRNSTPLHLAAGYNNLEVAEYLLEHGADVNAQDKGGLIPLHNAASYGHVDIAALLIKYNTCVNATDKWAFTPLHEAAQKGRTQLCALLLAHGADPTMKNQEGQTPLDLATADDIRALLIDAMPENLYFQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.502
R work: 0.1715
R free: 0.2072
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 289
Crystal growth procedure: 100 mM HEPES/sodium hydroxide, 200 mM sodium chloride, 20% (w/v) PEG 6000
Matthews coefficient: 2.15
Solvent content (%): 42.84
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: 2017-07-12
Alzheimer's Amyloid-Beta Peptide Fragment 1-40 in Complex with Cd-substituted Thermolysin (PDB entry 5ONP)
Macromolecule: Thermolysin
Type: Protein, polypeptide(L)
Source organism: Geobacillus stearothermophilus
EC number: 3.4.24.27
Sequence length: 316 residues
Sequence: ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGNGIFTYDAKYRTTLPGSLWADADNQFFASYDAPAVDAHYYAGVTYDYYKNVHNRLSYDGNNAAIRSSVHYSQGYNNAFWNGSQMVYGDGDGQTFIPLSGGIDVVAHELTHAVTDYTAGLIYQNESGAINEAISDIFGTLVEFYANKNPDWEIGEDVYTPGISGDSLRSMSDPAKYGDPDHYSKRYTGTQDNGGVHINSGIINKAAYLISQGGTHYGVSVVGIGRDKLGKIFYRALTQYLTPTSNFSQLRAAAVQSATDLYGSTSQEVASVKQAFDAVGVK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.34
R work: 0.161
R free: 0.1799
Average B factor: 18.1855
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 50 mM MES: 45% DMSO: 0.7-0.9 M NaCl: 0-0.4 M CdCl2: reservoir solution
containing 30-40% ammonium sulphate
Matthews coefficient: 2.36
Solvent content (%): 47.79
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2018-08-29
CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJB44355437 (PDB entry 7BO7)
Macromolecule: Protein arginine N-methyltransferase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.320
Sequence length: 645 residues
Sequence: MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.83
R work: 0.205
R free: 0.25
Average B factor: 64.138
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: PEG3350, 150mM ammonium sulfate
Matthews coefficient: 2.8
Solvent content (%): 56.02
Ligand: (2~{R},3~{R},4~{S},5~{R})-2-[(4~{a}~{S},7~{a}~{S})-4-azanyl-1,4,4~{a},7~{a}-tetrahydropyrrolo[2,3-d]pyrimidin-7-yl]-5-(quinolin-7-yloxymethyl)oxolane-3,4-diol (U6K)
Ligand formula: C20 H23 N5 O4
Ligand molecular weight: 397.428
Ligand SMILES: c1cc2ccc(cc2nc1)OCC3C(C(C(O3)N4C=CC5C4NC=NC5N)O)O
Ligand InChI: InChI=1S/C20H23N5O4/c21-18-13-5-7-25(19(13)24-10-23-18)20-17(27)16(26)15(29-20)9-28-12-4-3-11-2-1-6-22-14(11)8-12/h1-8,10,13,15-20,26-27H,9,21H2,(H,23,24)/t13-,15+,16+,17+,18+,19-,20+/m0/s1
Release date: 2022-03-02
Human PrimPol extending from the erroneous primer base A opposite the 8-oxoguanine lesion (PDB entry 7JLG)
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): 2.07
R work: 0.2007
R free: 0.2188
Average B factor: 77.2255
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: 2.28
Solvent content (%): 46.15
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
Crystal structure of human carbonic anhydrase isozyme II with inhibitor (PDB entry 4QIY)
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): 1.3
R work: 0.151
R free: 0.192
Average B factor: 16.645
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M sodium BICINE, pH 9, 0.2M ammonium sulfate, 2M sodium malonate pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Matthews coefficient: 2
Solvent content (%): 38.2
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: 2015-04-15
Crystal structure of JNK3 in complex with a fragment molecule (PDB entry 7YL1)
Macromolecule: Mitogen-activated protein kinase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 464 residues
Sequence: MSLHFLYYCSEPTLDVKIAFCQGFDKQVDVSYIAKHYNMSKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNSEEKTKNGVVKGQPSPSGAAVNSSESLPPSSSVNDISSMSTDQTLASDTDSSLEASAGPLGCCR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.48
R work: 0.20356
R free: 0.2944
Average B factor: 43.157
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.25
Crystallization temperature (K): 277
Crystal growth procedure: PEG MME 550, ethylene glycol, HEPES
Matthews coefficient: 1.84
Solvent content (%): 33.04
Ligand: 7-hexyl-3-methyl-8-sulfanylidene-9H-purine-2,6-dione (J6F)
Ligand formula: C12 H18 N4 O2 S
Ligand molecular weight: 282.362
Ligand SMILES: CCCCCCN1C2=C(NC1=S)N(C(=O)NC2=O)C
Ligand InChI: InChI=1S/C12H18N4O2S/c1-3-4-5-6-7-16-8-9(13-12(16)19)15(2)11(18)14-10(8)17/h3-7H2,1-2H3,(H,13,19)(H,14,17,18)
Release date: 2023-07-26
Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with 5-((3-(4H-1,2,4-triazol-4-yl)phenyl)amino)-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidine-3-carbonitrile (PDB entry 8P07)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 338 residues
Sequence: SMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.20401
R free: 0.25105
Average B factor: 61.686
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350
Matthews coefficient: 3.13
Solvent content (%): 60.74
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: 2023-05-17
Crystal structure of human GABARAP fused to EGFR (1076-1099) (PDB entry 8S1M)
Macromolecule: Epidermal growth factor receptor,Gamma-aminobutyric acid receptor-associated protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 145 residues
Sequence: GSALTEDSIDDTFLPVPEYINQSVPKGSMKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2033
R free: 0.2298
Average B factor: 72.05
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.17 M ammonium acetate
0.085 M sodium citrate
25.5% PEG 4000
15% Glycerol
Matthews coefficient: 2.56
Solvent content (%): 51.96
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: 2024-08-14
Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal (PDB entry 4YV8)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 215 residues
Sequence: APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.173
R free: 0.205
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 294.15
Crystal growth procedure: 24% PEG 8000, 0.2M ammonium sulfate
Matthews coefficient: 2.18
Solvent content (%): 43.59
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: 2016-05-04
Crystal structure of SETDB1 Tudor domain with aryl triazole fragment peptide conjugates (PDB entry 6BPI)
Macromolecule: Histone-lysine N-methyltransferase SETDB1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 213 residues
Sequence: ENLYFQGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYDYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSMK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.18785
R free: 0.19939
Average B factor: 25.147
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.2M LiSO4, 0.1M Bis-Tris pH 6.5
Matthews coefficient: 2.34
Solvent content (%): 47.48
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: 2017-12-27