satarupa22/MacromolecularLigandDB huggingface dataset:
HUMAN STEROL 14-ALPHA DEMETHYLASE (CYP51) IN COMPLEX WITH VFV IN P1 SPACE GROUP (PDB entry 4UHL)
Macromolecule: STEROL 14-ALPHA DEMETHYLASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.13.70
Sequence length: 446 residues
Sequence: GKLPPYIFSPIPFLGHAIAFGKSPIEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEDVYSRLTTPVFGKGVAYDVPNPVFLEQKKMLKSGLNIAHFKQHVSIIEKETKEYFESWGESGEKNVFEALSELIILTASHCLHGKEIRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKDIFYKAIQKRRQSQEKIDDILQTLLDATYKDGRPLTDDEVAGMLIGLLLAGQHTSSTTSAWMGFFLARDKTLQKKCYLEQKTVCGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIMMRMARTPQTVAGYTIPPGHQVCVSPTVNQRLKDSWVERLDFNPDRYLQDNPASGEKFAYVPFGAGRHRCIGENFAYVQIKTIWSTMLRLYEFDLIDGYFPTVNYTTMIHTPENPVIRYKRRSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.19013
R free: 0.2371
Average B factor: 64.354
Crystallization pH: 7.4
Crystal growth procedure: pH 7.4
Matthews coefficient: 2.7
Solvent content (%): 53.7
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: 2016-06-15
The ubiquitin-associated domain of human thirty-eight negative kinase-1 flexibly fused to the 1TEL crystallization chaperone via a GSGG linker (PDB entry 7T8J)
Macromolecule: Transcription factor ETV6,Non-receptor tyrosine-protein kinase TNK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 157 residues
Sequence: GSIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLSPIDSNTFEMNGKALLLLTKEDFRYRSPHSGDELYELLQHILGSGGELQRKIMEVELSVHGVTHQEAQTALGATGGDVVSAIRNLKVDQLFHLSSRSRADAWRILEHYQWDLSAASRYVLARP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.2238
R free: 0.2347
Average B factor: 56.32
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: 1.2 uL of 1 mg/mL protein in 50 mM Tris pH 8.8, 200 mM KCl combined with 1.2 uL of 100 mM Bis-tris-propane, 2.5 M Ammonium Nitrate
Matthews coefficient: 2.16
Solvent content (%): 43.06
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: 2022-12-21
crystal structure of human carbonic anhydrase I in complex with 4-(3-(2-((2-fluorobenzyl)amino)ethyl)ureido) benzenesulfonamide (PDB entry 6XZX)
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): 1.55
R work: 0.2002
R free: 0.2241
Average B factor: 32.56
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 200 mM Na-acetate, 30% PEG 4000, 100 mM Tris-HCl pH 9.
Inhibitor:150 mM NaCl, 10% DMSO,  50 mM Tris pH 7
Matthews coefficient: 2.33
Solvent content (%): 47.13
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: 2020-09-23
Crystal structure of PTPN3 (PTPH1) in complex with Eps15 pTyr849 P850V peptide (PDB entry 4S0G)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 306 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNADTLEGSMAQLKKGLESGTVLIQFEQLYRKKPGLAITFAKLPQNLDKNRYKDVLPYDTTRVLLQGNEDYINASYVNMEIPAANLVNKYIATQGPLPHTCAQFWQVVWDQKLSLIVMLTTLTERGRTKCHQYWPDPPDVMNHGGFHIQCQSEDCTIAYVSREMLVTNTQTGEEHTVTHLQYVAWPAHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHSSAGIGRTGVLVTMETAMCLTERNLPIYPLDIVRKMRDQRAMMVQTSSQYKFVCEAILRVYEEGLVQM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.723
R work: 0.1823
R free: 0.2285
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris-HCl, 26% PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Matthews coefficient: 1.87
Solvent content (%): 34.29
Release date: 2015-03-11
Crystal structure of PI3Kalpha inhibitor 4-0686 (PDB entry 7K71)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 946 residues
Sequence: GSVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2431
R free: 0.2586
Average B factor: 95.58
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 286
Crystal growth procedure: 8% (w/v) PEG 6000, 0.1 M CHES pH 9.75, 0.64 M sodium formate, 5 mM TCEP pH 7
Matthews coefficient: 2.57
Solvent content (%): 52.05
Ligand: 2-(morpholin-4-yl)[4,5'-bipyrimidin]-2'-amine (VYP)
Ligand formula: C12 H14 N6 O
Ligand molecular weight: 258.279
Ligand SMILES: c1cnc(nc1c2cnc(nc2)N)N3CCOCC3
Ligand InChI: InChI=1S/C12H14N6O/c13-11-15-7-9(8-16-11)10-1-2-14-12(17-10)18-3-5-19-6-4-18/h1-2,7-8H,3-6H2,(H2,13,15,16)
Release date: 2021-01-06
MEK1 in complex with compound 6 (PDB entry 7B3M)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 1,Dual specificity mitogen-activated protein kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 326 residues
Sequence: MAHHHHHHAAAENLYFQLEELELDEQQRKRLEAFLTQKQKVGELKDDDFEKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIGSGSGSMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.217
R free: 0.268
Average B factor: 26.21
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: MEK1 was prepared in buffer containing 25 mM Tris pH 7.5, 150 mM NaCl, 5% glycerol and 1 mM TCEP at a concentration of 10 mg/ml  mixed with 2 mM MgCl2 and 2 mM AMP-PNP, and incubated at room temperature for 30 minutes. Crystals were obtained from hanging drops by mixing a 1:1 ratio of protein solution with well solution containing 2 M AmSO4, 0.1 M NaCl and 0.1 M Bis-tris pH 6.1-6.2 at room temperature.
Matthews coefficient: 2.24
Solvent content (%): 45.02
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: 2021-03-03
STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH KETONE INHIBITOR (COMPOUND E) (PDB entry 6XEB)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 376 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1715
R free: 0.1929
Average B factor: 23.86
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
Matthews coefficient: 2.47
Solvent content (%): 50.23
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: 2020-08-12
Carbonic Anhydrase CAIX mimic in complex with inhibitor JS14 (PDB entry 6GXE)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.12489
R free: 0.15433
Average B factor: 15.254
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: Complex was prepared by adding 1-fold molar excess of inhibitor (dissolved in pure DMSO) to 25 mg/mL protein solution in water. 2 uL of complex solution were mixed with 1 uL of precipitant solution containing 1.6M sodium citrate, 50mM Tris H2SO4 pH 7.8
Matthews coefficient: 2.1
Solvent content (%): 41.34
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: 2019-05-08
Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI (PDB entry 5VK0)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 85 residues
Sequence: ETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.19793
R free: 0.24656
Average B factor: 26.736
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 294
Crystal growth procedure: 1340 mM ammonium sulfate,
6.7% glycerol, 50 mM magnesium sulfate,
100 mM imidazole pH 6.5
Matthews coefficient: 2.53
Solvent content (%): 51.46
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: 2018-04-25
Crystal Structure Analysis of human PRPK complex with a compound (PDB entry 7SZB)
Macromolecule: EKC/KEOPS complex subunit TP53RK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6
Sequence length: 255 residues
Sequence: GPMAAARATTPADGEEPAPEAEALAAARERSSRFLSGLELVKQGAEARVFRGRFQGRAAVIKHRFPKGYRHPALEARLGRRRTVQEARALLRCRRAGISAPVVFFVDYASNCLYMEEIEGSVTVRDYIQSTMETEKTPQGLSNLAKTIGQVLARMHDEDLIHGDLTTSNMLLKPPLEQLNIVLIDFGLSFISALPEDKGVDLYVLEKAFLSTHPNTETVFEAFLKSYSTSSKKARPVLKKLDEVRLRGRKRSMVG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.1698
R free: 0.209
Average B factor: 37.3591
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.2
Crystallization temperature (K): 293
Crystal growth procedure: 100mM Sodium citrate pH 5.2, 12.8% PEG8000, 10mM MgCl2, 10mM TCEP
Matthews coefficient: 2.25
Solvent content (%): 45.29
Ligand: 5-amino-2-[(3R)-2,6-dioxopiperidin-3-yl]-1H-isoindole-1,3(2H)-dione (DQ4)
Ligand formula: C13 H11 N3 O4
Ligand molecular weight: 273.244
Ligand SMILES: c1cc2c(cc1N)C(=O)N(C2=O)C3CCC(=O)NC3=O
Ligand InChI: InChI=1S/C13H11N3O4/c14-6-1-2-7-8(5-6)13(20)16(12(7)19)9-3-4-10(17)15-11(9)18/h1-2,5,9H,3-4,14H2,(H,15,17,18)/t9-/m1/s1
Release date: 2023-01-25
Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.7 A resolution (PDB entry 6JB6)
Macromolecule: Ubiquitin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 76 residues
Sequence: MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2436
R free: 0.2845
Average B factor: 40.89
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: HEPES, PEG 400, magnesium chloride
Matthews coefficient: 2.51
Solvent content (%): 51.06
Release date: 2019-03-20
Crystal structure of cysteine-bound ferrous form of the matured Cl2-Tyr157 human cysteine dioxygenase (PDB entry 6BPX)
Macromolecule: Cysteine dioxygenase type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.20
Sequence length: 200 residues
Sequence: SEQTEVLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKETLFAWPDKKSNEMVKKSERVLRENQCAYINDSVGLHRVENISHTEPAVSLHLXSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTPNATSGSLENN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1779
R free: 0.2124
Average B factor: 42.9168
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M MES, 2 M ammonium sulfate, 2% PEG400
Matthews coefficient: 3.73
Solvent content (%): 67.06
Ligand: FE (II) ION (FE2)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+2]
Ligand InChI: InChI=1S/Fe/q+2
Release date: 2018-07-04
VDR LBD complex with 25-nitro derivative of 1,25D3 (PDB entry 8CK5)
Macromolecule: Vitamin D3 receptor A
Type: Protein, polypeptide(L)
Source organism: Danio rerio
Sequence length: 302 residues
Sequence: GSHMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNHSPESVDTKLNFSNLLMMYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEVS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1905
R free: 0.2428
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate
Matthews coefficient: 2.28
Solvent content (%): 46.02
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2023-04-26
Crystal structure of CREBBP bromodomain complexd with PB08 (PDB entry 6FR0)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1783
R free: 0.2023
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Hepes, pH7.5, 0.2 M LiSO4, 25% PEG3350
Matthews coefficient: 2.01
Solvent content (%): 38.78
Ligand: ~{N}-[3-(5-ethanoyl-2-ethoxy-phenyl)-5-(2-ethyl-5-methyl-3-oxidanylidene-1,2-oxazol-4-yl)phenyl]furan-2-carboxamide (E3H)
Ligand formula: C27 H26 N2 O6
Ligand molecular weight: 474.505
Ligand SMILES: CCN1C(=O)C(=C(O1)C)c2cc(cc(c2)NC(=O)c3ccco3)c4cc(ccc4OCC)C(=O)C
Ligand InChI: InChI=1S/C27H26N2O6/c1-5-29-27(32)25(17(4)35-29)20-12-19(13-21(14-20)28-26(31)24-8-7-11-34-24)22-15-18(16(3)30)9-10-23(22)33-6-2/h7-15H,5-6H2,1-4H3,(H,28,31)
Release date: 2018-08-29
Gcase in complex with small molecule inhibitor 1 (PDB entry 9FB2)
Macromolecule: Lysosomal acid glucosylceramidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.45
Sequence length: 546 residues
Sequence: MEFSSPSREECPKPLSRVSIMAGSLTGLLLLQAVSWASGARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWRRQHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.14
R work: 0.15666
R free: 0.1724
Average B factor: 17.029
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M KSCN
25% PEG 3350
Matthews coefficient: 2.13
Solvent content (%): 42.33
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2024-07-03
Crystal Structure of Glycogen Synthase Kinase-3 beta in Complex with BI-91BS (PDB entry 6GJO)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 414 residues
Sequence: TTSFAESCKPVQQPSAFGSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARIQAAASTPTNATAASDANTGDRGQTNNAASASASNST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.91
R work: 0.217
R free: 0.237
Average B factor: 19.03
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.1
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Tris Acetate pH 8.1, 125 mM NaCl, 15-20% PEG8K
Matthews coefficient: 3.01
Solvent content (%): 59.15
Ligand: (3~{Z})-5-ethanoyl-3-[[(1-methylpiperidin-4-yl)amino]-phenyl-methylidene]-1~{H}-indol-2-one (F1B)
Ligand formula: C23 H25 N3 O2
Ligand molecular weight: 375.464
Ligand SMILES: CC(=O)c1ccc2c(c1)C(=C(c3ccccc3)NC4CCN(CC4)C)C(=O)N2
Ligand InChI: InChI=1S/C23H25N3O2/c1-15(27)17-8-9-20-19(14-17)21(23(28)25-20)22(16-6-4-3-5-7-16)24-18-10-12-26(2)13-11-18/h3-9,14,18,24H,10-13H2,1-2H3,(H,25,28)/b22-21-
Release date: 2019-03-27
Crystal Structure of BMP-2-inducible kinase in complex with an Indazole inhibitor (PDB entry 5I3R)
Macromolecule: BMP-2-inducible protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 302 residues
Sequence: RVFAVGRHQVTLEESLAEGGFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQVSYFAFKFAAADCPVSNINNSSIPSALPEPMTA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.185
R free: 0.231
Average B factor: 59.66
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293.15
Crystal growth procedure: 20% PEG 8000; 0.2 M Ammonium chloride; 10% Ethyleneglycol; 0.1M MES pH 6.0
Matthews coefficient: 2.88
Solvent content (%): 57.36
Ligand: N-[6-(3-{[(cyclopropylmethyl)sulfonyl]amino}phenyl)-1H-indazol-3-yl]cyclopropanecarboxamide (IDK)
Ligand formula: C21 H22 N4 O3 S
Ligand molecular weight: 410.489
Ligand SMILES: c1cc(cc(c1)NS(=O)(=O)CC2CC2)c3ccc4c(c3)[nH]nc4NC(=O)C5CC5
Ligand InChI: InChI=1S/C21H22N4O3S/c26-21(14-6-7-14)22-20-18-9-8-16(11-19(18)23-24-20)15-2-1-3-17(10-15)25-29(27,28)12-13-4-5-13/h1-3,8-11,13-14,25H,4-7,12H2,(H2,22,23,24,26)
Release date: 2016-03-09
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712 derivative ATDL18 (PDB entry 6Q7F)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.204
R work: 0.1868
R free: 0.2104
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 37.5 % MPD_PEG1000_PEG3350, 125 mM Morpheus Carboxylic Acids Mix, 100 mM Morpheus Buffer System 3 (Tris/Bicine)
Matthews coefficient: 1.95
Solvent content (%): 37.02
Ligand: 3-[(4-imidazol-1-yl-6-piperazin-1-yl-1,3,5-triazin-2-yl)amino]-4-methyl-~{N}-[3-(trifluoromethyl)phenyl]benzamide (HNZ)
Ligand formula: C25 H24 F3 N9 O
Ligand molecular weight: 523.513
Ligand SMILES: Cc1ccc(cc1Nc2nc(nc(n2)N3CCNCC3)n4ccnc4)C(=O)Nc5cccc(c5)C(F)(F)F
Ligand InChI: InChI=1S/C25H24F3N9O/c1-16-5-6-17(21(38)31-19-4-2-3-18(14-19)25(26,27)28)13-20(16)32-22-33-23(36-10-7-29-8-11-36)35-24(34-22)37-12-9-30-15-37/h2-6,9,12-15,29H,7-8,10-11H2,1H3,(H,31,38)(H,32,33,34,35)
Release date: 2020-01-15