satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure Analysis of human PIN1 (PDB entry 6VAJ)
Macromolecule: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 178 residues
Sequence: GSHMARGCRNSARGKMADEEKLPPGWEKRMSRSSGRVYYFNHITNASQWERPSGNSSSGGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEQITRTQEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.42
R work: 0.1923
R free: 0.2143
Average B factor: 31.7863
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100mM HEPES-7.5, 3.0M ammonium sulfate
Matthews coefficient: 2.03
Solvent content (%): 39.42
Ligand: 2-chloro-N-(2,2-dimethylpropyl)-N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]acetamide (QT7)
Ligand formula: C11 H20 Cl N O3 S
Ligand molecular weight: 281.799
Ligand SMILES: CC(C)(C)CN(C1CCS(=O)(=O)C1)C(=O)CCl
Ligand InChI: InChI=1S/C11H20ClNO3S/c1-11(2,3)8-13(10(14)6-12)9-4-5-17(15,16)7-9/h9H,4-8H2,1-3H3/t9-/m1/s1
Release date: 2020-12-30
Protein Tyrosine Phosphatase 1B L192A mutant, open state (PDB entry 5KA8)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 306 residues
Sequence: GHMASMEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFANFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.971
R work: 0.1883
R free: 0.2316
Average B factor: 33.9245
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES, pH 8.0, 0.2 M MgCl2, 19% PEG8000
Matthews coefficient: 3.6
Solvent content (%): 65.88
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: 2017-03-01
Crystal structure of MOZ double PHD finger domain in complex with histone H3 crotonylation at K14 (PDB entry 5B76)
Macromolecule: Histone acetyltransferase KAT6A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 131 residues
Sequence: SLPHEKDKPVAEPIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECKTCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRPRKKGRKLLQKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.653
R work: 0.1866
R free: 0.2365
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 290
Crystal growth procedure: polyethylene glycol 4000,  lithium sulfate, Tris
Matthews coefficient: 2.46
Solvent content (%): 50.07
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: 2016-10-26
Structure of WWP2 WW2-2,3-linker-HECT aa 334-398 linked to 485-865 (PDB entry 5TJ7)
Macromolecule: NEDD4-like E3 ubiquitin-protein ligase WWP2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 447 residues
Sequence: GPGWEKRTDPRGRFYYVDHNTRTTTWQRPTAEYVRNYEQWQSQRNQLQGAMQHFSQRFLYQSSSASQGSPGAYDRSFRWKYHQFRFLCHSNALPSHVKISVSRQTLFEDSFQQIMNMKPYDLRRRLYIIMRGEEGLDYGGIAREWFFLLSHEVLNPMYCLFEYAGKNNYCLQINPASSINPDHLTYFRFIGRFIAMALYHGKFIDTGFTLPFYKRMLNKRPTLKDLESIDPEFYNSIVWIKENNLEECGLELYFIQDMEILGKVTTHELKEGGESIRVTEENKEEYIMLLTDWRFTRGVEEQTKAFLDGFNEVAPLEWLRYFDEKELELMLCGMQEIDMSDWQKSTIYRHYTKNSKQIQWFWQVVKEMDNEKRIRLLQFVTGTCRLPVGGFAELIGSNGPQKFCIDKVGKETWLPRSHTCFNRLDLPPYKSYEQLREKLLYAIEETE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2072
R free: 0.2836
Average B factor: 23.905
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M potassium thiocyanate, 30% PEG monomethyl ether 2000
Matthews coefficient: 2.05
Solvent content (%): 40.02
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-05-31
Melatonin-Notum complex (PDB entry 6TR5)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.509
R work: 0.1964
R free: 0.2256
Average B factor: 27.4968
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.2
Crystallization temperature (K): 300
Crystal growth procedure: 1.5 M ammonium sulphate 
0.1 M sodium citrate pH 4.2
Matthews coefficient: 2
Solvent content (%): 38.46
Ligand: N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide (ML1)
Ligand formula: C13 H16 N2 O2
Ligand molecular weight: 232.278
Ligand SMILES: CC(=O)NCCc1c[nH]c2c1cc(cc2)OC
Ligand InChI: InChI=1S/C13H16N2O2/c1-9(16)14-6-5-10-8-15-13-4-3-11(17-2)7-12(10)13/h3-4,7-8,15H,5-6H2,1-2H3,(H,14,16)
Release date: 2020-01-15
Human angiogenin PD variant H13R (PDB entry 5M9A)
Macromolecule: Angiogenin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27
Sequence length: 124 residues
Sequence: MQDNSRYTHFLTQRYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFRRP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.23241
R free: 0.29676
Average B factor: 30.859
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.2 M Na/K tartrate
20% PEG 3350
Matthews coefficient: 1.83
Solvent content (%): 32.85
Ligand: D(-)-TARTARIC ACID (TAR)
Ligand formula: C4 H6 O6
Ligand molecular weight: 150.087
Ligand SMILES: C(C(C(=O)O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/t1-,2-/m0/s1
Release date: 2017-02-22
Carbonic Anhydrase IX mimic complexed with 4-(2-(3-(3,5-dimethylphenyl)ureido)ethylsulfonamido)benzenesulfonamide (PDB entry 7K6X)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.1798
R free: 0.2233
Average B factor: 20.2543
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 295
Crystal growth procedure: 1.6M Sodium Citrate, 50mM Tris, pH 6.4
Matthews coefficient: 2.12
Solvent content (%): 41.88
Ligand: 4-{[(2-{[(3,5-dimethylphenyl)carbamoyl]amino}ethyl)sulfonyl]amino}benzene-1-sulfonamide (VZ1)
Ligand formula: C17 H22 N4 O5 S2
Ligand molecular weight: 426.51
Ligand SMILES: Cc1cc(cc(c1)NC(=O)NCCS(=O)(=O)Nc2ccc(cc2)S(=O)(=O)N)C
Ligand InChI: InChI=1S/C17H22N4O5S2/c1-12-9-13(2)11-15(10-12)20-17(22)19-7-8-27(23,24)21-14-3-5-16(6-4-14)28(18,25)26/h3-6,9-11,21H,7-8H2,1-2H3,(H2,18,25,26)(H2,19,20,22)
Release date: 2020-12-23
Crystal Structure of EGFR LRTM with compound 7 (PDB entry 8D73)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 348 residues
Sequence: MGSSHHHHHHSSGENLYFQGSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.1914
R free: 0.2853
Average B factor: 50.276
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 285
Crystal growth procedure: 0.10 M sodium acetate, pH 5.8, 0.30 M potassium acetate, 15% glycerol, 9% PEG 8000
Matthews coefficient: 2.12
Solvent content (%): 42.11
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: 2022-07-27
Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, circular permutant P2/3 (PDB entry 5J0C)
Macromolecule: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],OXIDOREDUCTASE,Superoxide dismutase [Cu-Zn]
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.15.1.1
Sequence length: 114 residues
Sequence: MAPVKVWGSIKGLTEGLHGFHVHGAGGDLGNVTADKDGVADVSIEDSVISLSGDHSIIGRTLVVHEKAGAGAGSRLASGVIGIAQAGAGATKAVAVLKGDGPVQGIINFEQKES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1436
R free: 0.1863
Average B factor: 23.238
Crystallization method: EVAPORATION
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MIB buffer
pH 5.0
25 % w/v PEG 1500
Matthews coefficient: 2.36
Solvent content (%): 47.93
Release date: 2017-02-01
Crystal Structure of Human Carbonic Anhydrase II In-complex with Acetohexamide at 2.6 A Resolution (PDB entry 8J2O)
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): 2.6
R work: 0.17656
R free: 0.25858
Average B factor: 12.813
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization solution was comprised of Tris-HCl buffer (50 mM, pH=7.4), and 2.9 M ammonium sulfate in sitting drop vapor diffusion setup. Crystallization drop was comprised of hCA-II, Acetohexamide and reservoir buffer.  25% v/v glycerol was used as cryoprotectant.
Matthews coefficient: 2.05
Solvent content (%): 39.89
Ligand: 1-cyclohexyl-3-(4-ethanoylphenyl)sulfonyl-urea (TF9)
Ligand formula: C15 H20 N2 O4 S
Ligand molecular weight: 324.395
Ligand SMILES: CC(=O)c1ccc(cc1)S(=O)(=O)NC(=O)NC2CCCCC2
Ligand InChI: InChI=1S/C15H20N2O4S/c1-11(18)12-7-9-14(10-8-12)22(20,21)17-15(19)16-13-5-3-2-4-6-13/h7-10,13H,2-6H2,1H3,(H2,16,17,19)
Release date: 2024-04-24
Human PARP14 (ARTD8), catalytic fragment in complex with compound 3 (PDB entry 6WE3)
Macromolecule: Protein mono-ADP-ribosyltransferase PARP14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2
Sequence length: 194 residues
Sequence: SNADMKQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2369
R free: 0.2729
Average B factor: 42.385
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 1.6 M Ammonium sulfate, 0.1 M MES pH 6.5, 10% v/v Jeffamine M-600
Matthews coefficient: 2.77
Solvent content (%): 55.62
Ligand: 2-{[(trans-4-hydroxycyclohexyl)sulfanyl]methyl}-8-methylquinazolin-4(3H)-one (TZ7)
Ligand formula: C16 H20 N2 O2 S
Ligand molecular weight: 304.407
Ligand SMILES: Cc1cccc2c1N=C(NC2=O)CSC3CCC(CC3)O
Ligand InChI: InChI=1S/C16H20N2O2S/c1-10-3-2-4-13-15(10)17-14(18-16(13)20)9-21-12-7-5-11(19)6-8-12/h2-4,11-12,19H,5-9H2,1H3,(H,17,18,20)/t11-,12-
Release date: 2021-03-24
Crystal structure of TL11-113 bound to TAK1-TAB1 (PDB entry 5J8I)
Macromolecule: Mitogen-activated protein kinase kinase kinase 7/TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 chimera
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 314 residues
Sequence: SLHMIDYKEIEVEEVVGRGAFGVVCKAKWRAKDVAIKQIESESERKAFIVELRQLSRVNHPNIVKLYGACLNPVCLVMEYAEGGSLYNVLHGAEPLPYYTAAHAMSWCLQCSQGVAYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICDFGTACDIQTHMTNNKGSAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDEIGGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQHSLPPGEDGRVEPYVDFAEFYRLWSVDHGEQSVVTAP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.404
R work: 0.2226
R free: 0.2444
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.75M NaCitrate, 0.1M Tris-HCL, 0.2M NaCl, pH 7.0, 5mM Adenosine;
Matthews coefficient: 3.97
Solvent content (%): 69.02
Ligand: N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)oxy]phenyl}prop-2-enamide (6H4)
Ligand formula: C24 H25 Cl N6 O2
Ligand molecular weight: 464.947
Ligand SMILES: CN1CCN(CC1)c2ccc(cc2)Nc3ncc(c(n3)Oc4ccccc4NC(=O)C=C)Cl
Ligand InChI: InChI=1S/C24H25ClN6O2/c1-3-22(32)28-20-6-4-5-7-21(20)33-23-19(25)16-26-24(29-23)27-17-8-10-18(11-9-17)31-14-12-30(2)13-15-31/h3-11,16H,1,12-15H2,2H3,(H,28,32)(H,26,27,29)
Release date: 2017-02-15
STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INHIBITOR 4,5,6,7-TETRABROMOBENZOTRIAZOLE (PDB entry 8QCD)
Macromolecule: Casein kinase II subunit alpha'
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: MGSSHHHHHHSQDPMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.03
R work: 0.1437
R free: 0.1562
Average B factor: 7.66
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: THE CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WAS MIXED IN A 1:10 RATIO WITH A 20 MM SOLUTION OF 4,5,6,7-TETRABROMOBENZOTRIAZOLE (TBBT) IN DMSO. AFTER INCUBATION ON ICE FOR 30 MIN AND CENTRIFUGATION (16100 TIMES G FOR 2 MIN AT ROOM TEMPERATUR) 10 MIKROLITER OF THE SUPERNATANT WERE MIXED WITH 5 MIKORLITER OF THE RESERVOIR SOLUTION [900 MM LICL, 28% (W/V) PEG 6000, 100 MM TRIS/HCl, PH 8.5]. AFTER EQUILIBRATION, MICROSEEDING WAS CARRIED OUT TO INDUCE CRYSTAL GROWTH. SMALL CRYSTALS APPEARED AFTER ONE WEEK. ONE OF THEM WAS USED AS A MACROSEED TRANSFERING IT TO A SECOND DROP PREPARED IN THE SAME MANNER AS THE FIRST ONE. ALL CRSTALLIZATION STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.
Matthews coefficient: 2.61
Solvent content (%): 52.88
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: 2023-12-06
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor JOMBt (PDB entry 7TGS)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1702
R free: 0.1842
Average B factor: 22.3
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 298
Crystal growth procedure: 19% PEG 3350
0.5 M KH2PO4
1:3 ratio of protein to inhibitor
1 uL of protein:inhibitor complex was mixed with 1 uL of mother liquor
Matthews coefficient: 2.43
Solvent content (%): 49.48
Ligand: (4S,7R,11S,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-4-[(furan-2-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide (I3Q)
Ligand formula: C34 H45 N7 O8
Ligand molecular weight: 679.763
Ligand SMILES: c1ccc2c(c1)CC(=O)NC(CCNC(=O)C=CC(=O)N3CCCC(C3)C(=O)NC(C(=O)NC2)Cc4ccco4)C(=O)NCCOCCN
Ligand InChI: InChI=1S/C34H45N7O8/c35-12-17-48-18-14-37-33(46)27-11-13-36-29(42)9-10-31(44)41-15-3-7-25(22-41)32(45)40-28(20-26-8-4-16-49-26)34(47)38-21-24-6-2-1-5-23(24)19-30(43)39-27/h1-2,4-6,8-10,16,25,27-28H,3,7,11-15,17-22,35H2,(H,36,42)(H,37,46)(H,38,47)(H,39,43)(H,40,45)/b10-9+/t25-,27+,28+/m1/s1
Release date: 2022-08-24
Crystal structure of CK2a2 form-1 (PDB entry 5YWM)
Macromolecule: Casein kinase II subunit alpha'
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 339 residues
Sequence: GPLGSMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.939
R work: 0.1907
R free: 0.2435
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: PEG 4000, Lithium sulfate monohydrate
Matthews coefficient: 2.06
Solvent content (%): 36.49
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: 2018-12-05
Crystal Structure of EGFR(L858R/T790M/C797S) in complex with CH7233163 (PDB entry 6LUB)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 329 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGSLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.315
R work: 0.1856
R free: 0.2255
Average B factor: 60.6602
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 294
Crystal growth procedure: 1.0 M Succinic Acid, 1.0 %(w/v) Polyethylene glycol monomethyl ether 2000, 0.1 M HEPES
Matthews coefficient: 3.35
Solvent content (%): 63.32
Ligand: N-[2-(1-cyclopropylsulfonylpyrazol-4-yl)pyrimidin-4-yl]-7-(4-methylpiperazin-1-yl)-5-propan-2-yl-9-[2,2,2-tris(fluoranyl)ethoxy]pyrido[4,3-b]indol-3-amine (EUX)
Ligand formula: C31 H34 F3 N9 O3 S
Ligand molecular weight: 669.72
Ligand SMILES: CC(C)n1c2cc(cc(c2c3c1cc(nc3)Nc4ccnc(n4)c5cnn(c5)S(=O)(=O)C6CC6)OCC(F)(F)F)N7CCN(CC7)C
Ligand InChI: InChI=1S/C31H34F3N9O3S/c1-19(2)43-24-14-28(38-27-6-7-35-30(39-27)20-15-37-42(17-20)47(44,45)22-4-5-22)36-16-23(24)29-25(43)12-21(41-10-8-40(3)9-11-41)13-26(29)46-18-31(32,33)34/h6-7,12-17,19,22H,4-5,8-11,18H2,1-3H3,(H,35,36,38,39)
Release date: 2020-10-07
Crystal structure of human Vaccinia-related kinase 1 (VRK1) in complex with AMP-PNP (PDB entry 6AC9)
Macromolecule: Serine/threonine-protein kinase VRK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 370 residues
Sequence: MPRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.186
R free: 0.223
Average B factor: 41.22
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 27.5 % w/v PEG 3350, 0.2 M of ammonium sulfate, 0.1 M of HEPES (pH 7.0)
Matthews coefficient: 2.57
Solvent content (%): 52.15
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2018-12-26
Crystal structure of huBChE with N-((1-(2,3-dihydro-1H-inden-2-yl)piperidin-3-yl)methyl)-N-(2-(dimethylamino)ethyl)-2-naphthamide. (PDB entry 5NN0)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 529 residues
Sequence: EDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1689
R free: 0.2064
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 6.5
2.3 M Ammonium sulfate
Matthews coefficient: 3.18
Solvent content (%): 61.33
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: 2018-03-14