satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of human DPP3 in complex with endomorphin-2. (PDB entry 5EHH)
Macromolecule: Dipeptidyl peptidase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.14.4
Sequence length: 726 residues
Sequence: MADTQYILPNDIGVSSLDSREAFRLLSPTERLYAYHLSRAAWYGGLAVLLQTSPEAPYIYALLSRLFRAQDPDQLRQHALAEGLTEEEYQAFLVYAAGVYSNMGNYKSFGDTKFVPNLPKEKLERVILGSEAAQQHPEEVRGLWQTCGELMFSLEPRLRHLGLGKEGITTYFSGNCTMEDAKLAQDFLDSQNLSAYNTRLFKEVDGCGKPYYEVRLASVLGSEPSLDSEVTSKLKSYEFRGSPFQVTRGDYAPILQKVVEQLEKAKAYAANSHQGQMLAQYIESFTQGSIEAHKRGSRFWIQDKGPIVESYIGFIESYRDPFGSRGEFEGFVAVVNKAMSAKFERLVASAEQLLKELPWPPTFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPNYDDLRQTEGFKNVSLGNVLAVAYATQREKLTFLEEDDKDLYILWKGPSFDVQVGLHALLGHGSGKLFVQDEKGAFNFDQETVINPETGEQIQSWYRCGETWDSKFSTIASSYEECRAESVGLYLSLHPQVLEIFGFEGADAEDVIYVNWLNMVRAGLLALEFYTPEAFNWRQAHMQARFVILRVLLEAGEGLVTITPTTGSDGRPDARVRLDRSKIRSVGKPALERFLRRLQVLKSTGDVAGGRALYEGYATVTDAPPESFLTLRDTVLLRKESRKLIVQPNTRLEGSDVQLLEYEASAAGLIRSFSERFPEDGPELEEILTQLATADARFW
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.1938
R free: 0.237
Average B factor: 37.4
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.2
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH-8.2.
Matthews coefficient: 2.49
Solvent content (%): 50.66
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: 2016-04-13
HUMAN PRMT5:MEP50 Crystal Structure With MTA and Fragment Bound (PDB entry 7ZV2)
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): 2.01
R work: 0.2323
R free: 0.2754
Average B factor: 33.111
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 16% PEG3350, 100 mM Na citrate pH 5.4, 100mM Carboxylic acids
Matthews coefficient: 2.91
Solvent content (%): 57.72
Ligand: 5'-DEOXY-5'-METHYLTHIOADENOSINE (MTA)
Ligand formula: C11 H15 N5 O3 S
Ligand molecular weight: 297.334
Ligand SMILES: CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
Release date: 2022-10-19
The FK1 domain of FKBP51 in complex with SAFit-analog 23b (PDB entry 9EUC)
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): 2.4
R work: 0.2505
R free: 0.2788
Average B factor: 46.746
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 14% PEG3350, 0.2M sodium thiocyanate, 0.1M HEPES-NaOH pH 7.5 10% ethylene glycol
Matthews coefficient: 2.41
Solvent content (%): 49.06
Ligand: (1-ethylpyrazol-4-yl)methyl (2S)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate (A1H7F)
Ligand formula: C29 H41 N3 O6
Ligand molecular weight: 527.652
Ligand SMILES: CCn1cc(cn1)COC(=O)C2CCCCN2C(=O)C(c3cc(c(c(c3)OC)OC)OC)C4CCCCC4
Ligand InChI: InChI=1S/C29H41N3O6/c1-5-31-18-20(17-30-31)19-38-29(34)23-13-9-10-14-32(23)28(33)26(21-11-7-6-8-12-21)22-15-24(35-2)27(37-4)25(16-22)36-3/h15-18,21,23,26H,5-14,19H2,1-4H3/t23-,26-/m0/s1
Release date: 2024-06-12
Structure of the kinase domain of human DDR1 in complex with a 2-Amino-2,3-Dihydro-1H-Indene-5-Carboxamide-based inhibitor (PDB entry 6HP9)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 315 residues
Sequence: SMPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDGQAAQGPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.2046
R free: 0.2507
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 1:2 protein to mother liquor

Protein: 
12 mg/ml in 50 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM TCEP, 2% DMSO, 1 mM compound

Mother liquor:
25% PEG 1500
Matthews coefficient: 2.4
Solvent content (%): 48.79
Ligand: (2~{R})-~{N}-[3-(4-methylimidazol-1-yl)-5-(trifluoromethyl)phenyl]-2-(pyrimidin-5-ylamino)-2,3-dihydro-1~{H}-indene-5-carboxamide (GKB)
Ligand formula: C25 H21 F3 N6 O
Ligand molecular weight: 478.469
Ligand SMILES: Cc1cn(cn1)c2cc(cc(c2)NC(=O)c3ccc4c(c3)CC(C4)Nc5cncnc5)C(F)(F)F
Ligand InChI: InChI=1S/C25H21F3N6O/c1-15-12-34(14-31-15)23-8-19(25(26,27)28)7-21(9-23)33-24(35)17-3-2-16-5-20(6-18(16)4-17)32-22-10-29-13-30-11-22/h2-4,7-14,20,32H,5-6H2,1H3,(H,33,35)/t20-/m1/s1
Release date: 2019-01-30
Bruton's tyrosine kinase in complex with 3-{[4-(1-acetylpiperidin-4-yl)phenyl]amino}-5-[(3R)-3-(3-methyl-2-oxoimidazolidin-1-yl)piperidin-1-yl]pyrazine-2-carboxamide (PDB entry 8EJB)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 270 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.58
R work: 0.1681
R free: 0.191
Average B factor: 20.72
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.02 M sodium formate, 0.02 M ammonium acetate,
0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0.02 M sodium oxamate 0.1 M MES/imidazole pH 6.5
Matthews coefficient: 2.42
Solvent content (%): 49.2
Ligand: 5-[(3R)-3-(3-methyl-2-oxoimidazolidin-1-yl)piperidin-1-yl]-3-[4-(piperidin-4-yl)anilino]pyrazine-2-carboxamide (WKC)
Ligand formula: C25 H34 N8 O2
Ligand molecular weight: 478.59
Ligand SMILES: CN1CCN(C1=O)C2CCCN(C2)c3cnc(c(n3)Nc4ccc(cc4)C5CCNCC5)C(=O)N
Ligand InChI: InChI=1S/C25H34N8O2/c1-31-13-14-33(25(31)35)20-3-2-12-32(16-20)21-15-28-22(23(26)34)24(30-21)29-19-6-4-17(5-7-19)18-8-10-27-11-9-18/h4-7,15,18,20,27H,2-3,8-14,16H2,1H3,(H2,26,34)(H,29,30)/t20-/m1/s1
Release date: 2023-02-15
Co-complex CYP46A1 with 0431 (compound 17) (PDB entry 7N3M)
Macromolecule: Cholesterol 24-hydroxylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.25
Sequence length: 474 residues
Sequence: MHHHHHHSRYEHIPGPPRPSFLLGHLPCFWKKDEVGGRVLQDVFLDWAKKYGPVVRVNVFHKTSVIVTSPESVKKFLMSTKYNKDSKMYRALQTVFGERLFGQGLVSECNYERWHKQRRVIDLAFSRSSLVSLMETFNEKAEQLVEILEAKADGQTPVSMQDMLTYTAMDILAKAAFGMETSMLLGAQKPLSQAVKLMLEGITASRNTLAKFLPGKRKQLREVRESIRFLRQVGRDWVQRRREALKRGEEVPADILTQILKAEEGAQDDEGLLDNFVTFFIAGHETSANHLAFTVMELSRQPEIVARLQAEVDEVIGSKRYLDFEDLGRLQYLSQVLKESLRLYPPAWGTFRLLEEETLIDGVRVPGNTPLLFSTYVMGRMDTYFEDPLTFNPDRFGPGAPKPRFTYFPFSLGHRSCIGQQFAQMEVKVVMAKLLQRLEFRLVPGQRFGLQEQATLKPLDPVLCTLRPRGWQPA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.698
R work: 0.1642
R free: 0.1918
Average B factor: 22.586
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 17.5% PEG 3350, 0.4M Calcium Cl
Matthews coefficient: 2.33
Solvent content (%): 42.62
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2022-02-23
Structure of UCHL1 in complex with GK13S inhibitor (PDB entry 7ZM0)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase isozyme L1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 227 residues
Sequence: GPGSMQLKPMEINPEMLNKVLSRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDGSVLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPVNHGASSEDTLLKDAAKVCREFTEREQGEVRFSAVALCKAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.2401
R free: 0.2878
Average B factor: 62.73
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.3 M ammonium sulphate, 110 mM K3PO4 and 90 mM K2HPO4
Matthews coefficient: 2.32
Solvent content (%): 46.87
Ligand: (3S)-1-(iminomethyl)-N-[1-[4-(pent-4-ynylcarbamoyl)phenyl]imidazol-4-yl]pyrrolidine-3-carboxamide (JMF)
Ligand formula: C21 H24 N6 O2
Ligand molecular weight: 392.454
Ligand SMILES: C#CCCCNC(=O)c1ccc(cc1)n2cc(nc2)NC(=O)C3CCN(C3)C=N
Ligand InChI: InChI=1S/C21H24N6O2/c1-2-3-4-10-23-20(28)16-5-7-18(8-6-16)27-13-19(24-15-27)25-21(29)17-9-11-26(12-17)14-22/h1,5-8,13-15,17,22H,3-4,9-12H2,(H,23,28)(H,25,29)/b22-14+/t17-/m0/s1
Release date: 2022-09-14
Crystal structure of yeast N-terminal acetyltransferase NatE (IP6) in complex with a bisubstrate (PDB entry 4XNH)
Macromolecule: N-terminal acetyltransferase A complex subunit NAT1
Type: Protein, polypeptide(L)
Source organism: Saccharomyces cerevisiae
Sequence length: 854 residues
Sequence: MSRKRSTKPKPAAKIALKKENDQFLEALKLYEGKQYKKSLKLLDAILKKDGSHVDSLALKGLDLYSVGEKDDAASYVANAIRKIEGASASPICCHVLGIYMRNTKEYKESIKWFTAALNNGSTNKQIYRDLATLQSQIGDFKNALVSRKKYWEAFLGYRANWTSLAVAQDVNGERQQAINTLSQFEKLAEGKISDSEKYEHSECLMYKNDIMYKAASDNQDKLQNVLKHLNDIEPCVFDKFGLLERKATIYMKLGQLKDASIVYRTLIKRNPDNFKYYKLLEVSLGIQGDNKLKKALYGKLEQFYPRCEPPKFIPLTFLQDKEELSKKLREYVLPQLERGVPATFSNVKPLYQRRKSKVSPLLEKIVLDYLSGLDPTQDPIPFIWTNYYLSQHFLFLKDFPKAQEYIDAALDHTPTLVEFYILKARILKHLGLMDTAAGILEEGRQLDLQDRFINCKTVKYFLRANNIDKAVEVASLFTKNDDSVNGIKDLHLVEASWFIVEQAEAYYRLYLDRKKKLDDLASLKKEVESDKSEQIANDIKENQWLVRKYKGLALKRFNAIPKFYKQFEDDQLDFHSYCMRKGTPRAYLEMLEWGKALYTKPMYVRAMKEASKLYFQMHDDRLKRKSDSLDENSDEIQNNGQNSSSQKKKAKKEAAAMNKRKETEAKSVAAYPSDQDNDVFGEKLIETSTPMEDFATEFYNNYSMQVREDERDYILDFEFNYRIGKLALCFASLNKFAKRFGTTSGLFGSMAIVLLHATRNDTPFDPILKKVVTKSLEKEYSENFPLNEISNNSFDWLNFYQEKFGKNDINGLLFLYRYRDDVPIGSSNLKEMIISSLSPLEPHSQNEILQYYL
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1682
R free: 0.2277
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 14% PEG 400, 0.1 M MES, pH 6.0
Matthews coefficient: 2.45
Solvent content (%): 49.71
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: 2016-07-20
Crystal structure of UBR box of YIFS-UBR4 (PDB entry 8J9R)
Macromolecule: E3 ubiquitin-protein ligase UBR4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 74 residues
Sequence: YIFSKLCTFTITQKEFMNQHWYHCHTCKMVDGVGVCTVCAKVCHKDHEISYAKYGSFFCDCGAKEDGSCLALVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.2342
R free: 0.2871
Average B factor: 19.04
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1 M Bis-Tris (pH5.6), 29% (w/v) polyethylene glycol 3350 (PEG3350), 0.2 M lithium sulfate monohydrate
Matthews coefficient: 2.3
Solvent content (%): 46.58
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: 2023-12-06
Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcDMJ and hexatungstotellurate(VI) TEW (PDB entry 6ZJ5)
Macromolecule: Glycoprotein endo-alpha-1,2-mannosidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.130
Sequence length: 382 residues
Sequence: MNHKVHHHHHHIEGRHMPLNNYLHVFYYSWYGNPQFDGKYIHWNHPVLEHWDPRIAKNYPQGRHNPPDDIGSSFYPELGSYSSRDPSVIETHMRQMRSASIGVLALSWYPPDVNDENGEPTDNLVPTILDKAHKYNLKVTFHIEPYSNRDDQNMYKNVKYIIDKYGNHPAFYRYKTKTGNALPMFYVYDSYITKPEKWANLLTTSGSRSIRNSPYDGLFIALLVEEKHKYDILQSGFDGIYTYFATNGFTYGSSHQNWASLKLFCDKYNLIFIPSVGPGYIDTSIRPWNTQNTRNRINGKYYEIGLSAALQTRPSLISITSFNEWHEGTQIEKAVPKRTSNTVYLDYRPHKPGLYLELTRKWSEKYSKERATYALDRQLPVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.269
R work: 0.1882
R free: 0.2559
Average B factor: 29.85
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 100 mM HEPES pH 7.5 - 8.1, 200 mM MgCl2, 25-27.5% v/v PEG 400, 1 mM TEW
Protein in 25 mM HEPES pH 7.0, 200 mM NaCl buffer at 10 mg/ml.
Matthews coefficient: 2.57
Solvent content (%): 52.2
Ligand: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE)
Ligand formula: C8 H18 N2 O4 S
Ligand molecular weight: 238.305
Ligand SMILES: C1CN(CCN1CCO)CCS(=O)(=O)O
Ligand InChI: InChI=1S/C8H18N2O4S/c11-7-5-9-1-3-10(4-2-9)6-8-15(12,13)14/h11H,1-8H2,(H,12,13,14)
Release date: 2020-12-09
Crystal structure of LSD1-CoREST in complex with PRSFLVRRK peptide (PDB entry 7CDF)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.66
Sequence length: 669 residues
Sequence: GPLGSHMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.21352
R free: 0.2406
Average B factor: 82.889
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
Ligand: FLAVIN-ADENINE DINUCLEOTIDE (FAD)
Ligand formula: C27 H33 N9 O15 P2
Ligand molecular weight: 785.55
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
Ligand InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
Release date: 2021-06-23
Structure of human NTHL1 - linker 1 chimera (PDB entry 7RDT)
Macromolecule: Isoform 3 of Endonuclease III-like protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 250 residues
Sequence: MLRVAYEGSDSEKGEGAEPLKVPVWEPQDWQQQLVNIRAMRNKKDAPTTELNFSSPKVRRYQVLLSLMLSSQTKDQVTAGAMQRLRARGLTVDSILQTDDATLGKLIYPVGFWRSKVKYIKQTSAILQQHYGGDIPASVAELVALPGVGPKMAHLAMAVAWGTVSGIAVDTHVHRIANRLRWTKKATKSPEETRAALEEWLPRELWHEINGLLVGFGQQTCLPVHPRCHACLNQALCPAAQGLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1812
R free: 0.2306
Average B factor: 29.49
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 291
Crystal growth procedure: PEG 6K, Sodium chloride, Tricine,
Matthews coefficient: 2.35
Solvent content (%): 47.7
Ligand: IRON/SULFUR CLUSTER (SF4)
Ligand formula: Fe4 S4
Ligand molecular weight: 351.64
Ligand SMILES: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
Ligand InChI: InChI=1S/4Fe.4S
Release date: 2021-12-29
PDE2 catalytic domain complexed with inhibitors (PDB entry 5U7D)
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): 1.75
R work: 0.1676
R free: 0.197
Average B factor: 32.7
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: 2.21
Solvent content (%): 44.45
Ligand: 2-(3,4-dimethoxybenzyl)-7-[(2R,3R)-2-hydroxy-6-phenylhexan-3-yl]-5-methylimidazo[5,1-f][1,2,4]triazin-4(3H)-one (19F)
Ligand formula: C27 H32 N4 O4
Ligand molecular weight: 476.567
Ligand SMILES: Cc1c2n(c(n1)C(CCCc3ccccc3)C(C)O)N=C(NC2=O)Cc4ccc(c(c4)OC)OC
Ligand InChI: InChI=1S/C27H32N4O4/c1-17-25-27(33)29-24(16-20-13-14-22(34-3)23(15-20)35-4)30-31(25)26(28-17)21(18(2)32)12-8-11-19-9-6-5-7-10-19/h5-7,9-10,13-15,18,21,32H,8,11-12,16H2,1-4H3,(H,29,30,33)/t18-,21+/m1/s1
Release date: 2017-06-28
CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Bosutinib isomer (PDB entry 5VCZ)
Macromolecule: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 311 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMHQLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1478
R free: 0.1814
Average B factor: 24.4034
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 14 MG/ML MYT1, 50 mM HEPES PH 7.5, 0.5 mM DTT, 0.05 M POTASSIUM CHLORIDE, 17.5 (V/V) % pentaerythritol propoxylate (5/4 PO/OH), 1.5 mM osutinib isomer
Matthews coefficient: 2.11
Solvent content (%): 41.67
Ligand: 4-[(3,5-DICHLORO-4-METHOXYPHENYL)AMINO]-6-METHOXY-7-[3-(4-METHYLPIPERAZIN-1-YL)PROPOXY]QUINOLINE-3-CARBONITRILE (XZN)
Ligand formula: C26 H29 Cl2 N5 O3
Ligand molecular weight: 530.446
Ligand SMILES: CN1CCN(CC1)CCCOc2cc3c(cc2OC)c(c(cn3)C#N)Nc4cc(c(c(c4)Cl)OC)Cl
Ligand InChI: InChI=1S/C26H29Cl2N5O3/c1-32-6-8-33(9-7-32)5-4-10-36-24-14-22-19(13-23(24)34-2)25(17(15-29)16-30-22)31-18-11-20(27)26(35-3)21(28)12-18/h11-14,16H,4-10H2,1-3H3,(H,30,31)
Release date: 2017-08-23
Crystal structure of human Fibrillarin in complex with compound 1 from single soak (PDB entry 7SE9)
Macromolecule: rRNA 2'-O-methyltransferase fibrillarin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 242 residues
Sequence: SNAGKNVMVEPHRHEGVFICRGKEDALVTKNLVPGESVYGEKRVSISEGDDKIEYRAWNPFRSKLAAAILGGVDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHRSGRDLINLAKKRTNIIPVIEDARHPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIKANCIDSTASAEAVFASEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPPKVKN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1871
R free: 0.2216
Average B factor: 27.91
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.75-3.3 M Sodium Formate
Matthews coefficient: 3.03
Solvent content (%): 59.36
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2022-02-09
Crystal Structure of human phosphodiesterase 10 in complex with 2,3-dimethyl-6-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-7-(trifluoromethyl)imidazo[1,2-b]pyridazine (PDB entry 5SGN)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.1721
R free: 0.2221
Average B factor: 40.469
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.63
Solvent content (%): 53.28
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: 2022-10-12