satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of pseudokinase CASK in complex with compound 25 (PDB entry 7OAL)
Macromolecule: Peripheral plasma membrane protein CASK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 353 residues
Sequence: SMGSPGISGGGGGIRTMADDDVLFEDVYELCEVIGKGPFSVVRRCINRETGQQFAVKIVDVAKFTSSPGLSTEDLKREASICHMLKHPHIVELLETYSSDGMLYMVFEFMDGADLCFEIVKRADAGFVYSEAVASHYMRQILEALRYCHDNNIIHRDVKPHCVLLASKENSAPVKLGGFGVAIQLGESGLVAGGRVGTPHFMAPEVVKREPYGKPVDVWGCGVILFILLSGCLPFYGTKERLFEGIIKGKYKMNPRQWSHISESAKDLVRRMLMLDPAERITVYEALNHPWLKERDRYAYKIHLPETVEQLRKFNARRKLKGAVLAAVSSHKFNSFYGDPPEELPDFSEDPTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.2206
R free: 0.2744
Average B factor: 38.404
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293.15
Crystal growth procedure: 9% high molecular weight PEG Smears, 0.1 M magnesium acetate, 0.1 M KCl, 0.1 M MES, pH 6.0
Matthews coefficient: 2.18
Solvent content (%): 43.55
Ligand: 2-[[2,5-bis(bromanyl)-4-methyl-phenyl]methylamino]-4-(cyclohexylamino)-N-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide (V62)
Ligand formula: C25 H32 Br2 N6 O3
Ligand molecular weight: 624.368
Ligand SMILES: Cc1cc(c(cc1Br)CNc2ncc(c(n2)NC3CCCCC3)C(=O)NCCCN4CCOC4=O)Br
Ligand InChI: InChI=1S/C25H32Br2N6O3/c1-16-12-21(27)17(13-20(16)26)14-29-24-30-15-19(22(32-24)31-18-6-3-2-4-7-18)23(34)28-8-5-9-33-10-11-36-25(33)35/h12-13,15,18H,2-11,14H2,1H3,(H,28,34)(H2,29,30,31,32)
Release date: 2021-05-19
Human poly(ADP-ribose) glycohydrolase in complex with synthetic dimeric ADP-ribose (PDB entry 5A7R)
Macromolecule: POLY(ADP-RIBOSE) GLYCOHYDROLASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.143
Sequence length: 531 residues
Sequence: GSSPDKKWLGTPIEEMRRMPRCGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPVEDENGERTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLAAAMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTAAAPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQENIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSHEDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESCAETADHSGQRTGT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1373
R free: 0.1789
Average B factor: 22.196
Crystallization pH: 8
Crystal growth procedure: 20% PEG3350, 0.2 M AMMONIUM SULFATE, 0.1 M PCTP PH 7.5
Matthews coefficient: 2.54
Solvent content (%): 51
Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL
[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE (AR6)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
Release date: 2015-07-22
Crystal structure of BACE complex with BMC008 (PDB entry 5QCY)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 402 residues
Sequence: GPDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.169
R free: 0.203
Average B factor: 47.57
Crystallization method: hanging drop
Crystallization temperature (K): 292
Crystal growth procedure: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM SULFATE. PROTEIN STOCK WAS BACE
MUT46B BATCH XII 8.45MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 5-FOLD EXCESS OF BMC008 ADDED FROM A 50MM STOCK
SOLUTION IN DMSO (2.0% DMSO IN DROP). CRYO- PROTECTANT WAS 1.2M AMMONIUM SULFATE, 25%(V/V)GLYCEROL, 2.0% DMSO, 1MM
BMC008.
Matthews coefficient: 3.08
Solvent content (%): 60.11
Ligand: (9R,11S)-11-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-9-methyl-16-(1,3-oxazol-2-yl)-3-[(1R)-1-phenylethyl]-3,12-diazabicyclo[12.3.1]octadeca-1(18),14,16-triene-2,13-dione (E5P)
Ligand formula: C40 H50 N4 O4
Ligand molecular weight: 650.849
Ligand SMILES: CC1CCCCCN(C(=O)c2cc(cc(c2)C(=O)NC(C1)C(CNCc3cccc(c3)C(C)C)O)c4ncco4)C(C)c5ccccc5
Ligand InChI: InChI=1S/C40H50N4O4/c1-27(2)32-16-11-13-30(21-32)25-41-26-37(45)36-20-28(3)12-7-6-10-18-44(29(4)31-14-8-5-9-15-31)40(47)35-23-33(38(46)43-36)22-34(24-35)39-42-17-19-48-39/h5,8-9,11,13-17,19,21-24,27-29,36-37,41,45H,6-7,10,12,18,20,25-26H2,1-4H3,(H,43,46)/t28-,29-,36+,37-/m1/s1
Release date: 2020-06-03