satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S (PDB entry 6BDT)
Macromolecule: Calpain-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.54
Sequence length: 382 residues
Sequence: IISRNFPIIGVKEKTFEQLHKKCLEKKVLYVDPEFPPDETSLFYSQKFPIQFVWKRPPEICENPRFIIDGANRTDICQGELGDSWFLAAIACLTLNQHLLFRVIPHDQSFIENYAGIFHFQFWRYGEWVDVVIDDCLPTYNNQLVFTKSNHRNEFWSALLEKAYAKLHGSYEALKGGNTTEAMEDFTGGVAEFFEIRDAPSDMYKIMKKAIERGSLMGCSIDDGTNMTYGTSPSGLNMGELIARMVRNMDNSLLQDSDLDPRGSDERPTRTIIPVQYETRMACGLVRGHAYSVTGLDEVPFKGEKVKLVRLRNPWGQVEWNGSWSDRWKDWSFVDKDEKARLQHQVTEDGEFWMSYEDFIYHFTKLEICNLTADLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2219
R free: 0.256
Average B factor: 60.172
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295.15
Crystal growth procedure: PEG 8000, MES, calcium chloride
Matthews coefficient: 2
Solvent content (%): 38.37
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: 2018-02-07
Human carbonic anhydrase II (F131Y/L198A) complexed with 1,3-thiazole-2-sulfonamide (PDB entry 5JGT)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 259 residues
Sequence: AHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDYGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSATTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.1194
R free: 0.1378
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: We soaked monoclinic crystals of HCAII with BTA by carrying out the following steps: (i) We prepared soaking solutions containing 1.32 M sodium citrate, 1 mM ZnSO4, 100 mM Tris-HCl (pH 7.8), and 5 mM ligand. (ii) We combined 4 uL of soaking solution and 1-2 crystals of HCAII within a drop on the surface of a reservoir cover (EasyXtal CrystalSupport, Qiagen). (iii) To a clear plastic reservoir in a 15-reservoir plate (EasyXtal, Qiagen), we added 1 mL of soaking solution (without ligand present). We attached the reservoir cover to the reservoir and left the entire setup at 4 deg C for 1 week.
Matthews coefficient: 2.12
Solvent content (%): 41.86
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: 2017-01-11
GTPase HRAS under 500 MPa pressure (PDB entry 7OGB)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 166 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.177
R free: 0.236
Average B factor: 24.22
Crystallization method: BATCH MODE
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 40 mM Tris HCL, 10 mM MgCl2, 2 mM DTE, 26-30 % PEG-400
Matthews coefficient: 1.9
Solvent content (%): 35.14
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2022-02-09
The FK1 domain of FKBP51 in complex with SAFit-analog 23j (PDB entry 9EU6)
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): 1.54
R work: 0.1931
R free: 0.2224
Average B factor: 24.975
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 45% Pentaerythritol propoxylate 5/4 PO/OH, 15% ethanol
Matthews coefficient: 2.25
Solvent content (%): 45.32
Ligand: (1,5-dimethylpyrazol-4-yl)methyl (2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate (A1H7U)
Ligand formula: C29 H41 N3 O6
Ligand molecular weight: 527.652
Ligand SMILES: Cc1c(cnn1C)COC(=O)C2CCCCN2C(=O)C(c3cc(c(c(c3)OC)OC)OC)C4CCCCC4
Ligand InChI: InChI=1S/C29H41N3O6/c1-19-22(17-30-31(19)2)18-38-29(34)23-13-9-10-14-32(23)28(33)26(20-11-7-6-8-12-20)21-15-24(35-3)27(37-5)25(16-21)36-4/h15-17,20,23,26H,6-14,18H2,1-5H3/t23-,26-/m0/s1
Release date: 2024-06-12
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000382a (PDB entry 7GSU)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1885
R free: 0.2201
Average B factor: 36.303
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.33
Solvent content (%): 63.05
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
SYK Kinase domain in complex with azabenzimidazole inhibitor 3 (PDB entry 6ZCS)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 299 residues
Sequence: MDTEVYESPYADPEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47
R work: 0.19
R free: 0.208
Average B factor: 29.18
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 0.1M Na3Cit pH 6.4, 16% PEG3350, 0.2M KH2PO4
Matthews coefficient: 2.27
Solvent content (%): 45.72
Ligand: (3~{R},4~{R})-~{N}4-[1-[2-(1-methylindol-4-yl)-3~{H}-imidazo[4,5-b]pyridin-7-yl]pyrazol-4-yl]oxane-3,4-diamine (QFE)
Ligand formula: C23 H24 N8 O
Ligand molecular weight: 428.49
Ligand SMILES: Cn1ccc2c1cccc2c3[nH]c4c(n3)c(ccn4)n5cc(cn5)NC6CCOCC6N
Ligand InChI: InChI=1S/C23H24N8O/c1-30-9-6-15-16(3-2-4-19(15)30)22-28-21-20(5-8-25-23(21)29-22)31-12-14(11-26-31)27-18-7-10-32-13-17(18)24/h2-6,8-9,11-12,17-18,27H,7,10,13,24H2,1H3,(H,25,28,29)/t17-,18+/m0/s1
Release date: 2021-06-23
Human Aldose Reductase complexed with Schl7764 at 1.12 A (PDB entry 4NKC)
Macromolecule: Aldose reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.21
Sequence length: 315 residues
Sequence: ASRILLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.12
R work: 0.1222
R free: 0.1419
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: di-Ammoniumhydrogen citrate,  
PEG6000= 5 % (m/V), DTT= 5,15 g/L, NADP+= 0,66 g/L    
Human Aldose Reductase= 15 mg/ml.    
Afterwards soaked into MES buffer, MES 50 mM 25% (m/V) PEG6000, saturated with the inhibitor, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 2.15
Solvent content (%): 42.92
Ligand: (2Z)-3-(3'-nitrobiphenyl-3-yl)prop-2-enoic acid (2HZ)
Ligand formula: C15 H11 N O4
Ligand molecular weight: 269.252
Ligand SMILES: c1cc(cc(c1)c2cccc(c2)[N+](=O)[O-])C=CC(=O)O
Ligand InChI: InChI=1S/C15H11NO4/c17-15(18)8-7-11-3-1-4-12(9-11)13-5-2-6-14(10-13)16(19)20/h1-10H,(H,17,18)/b8-7-
Release date: 2015-03-04
The co-crystal structure of DYRK2 with a small molecule inhibitor 18 (PDB entry 7DL6)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 324 residues
Sequence: HDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTYIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.648
R work: 0.1711
R free: 0.2322
Average B factor: 46.2211
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.36 M-0.5 M sodium citrate tribasic dehydrate, 0.01 M sodium borate, pH7.5-9.5
Matthews coefficient: 3.65
Solvent content (%): 66.34
Ligand: [2,7-dimethoxy-9-[[(3R)-pyrrolidin-3-yl]methylsulfanyl]acridin-4-yl]methanol (H96)
Ligand formula: C21 H24 N2 O3 S
Ligand molecular weight: 384.492
Ligand SMILES: COc1ccc2c(c1)c(c3cc(cc(c3n2)CO)OC)SCC4CCNC4
Ligand InChI: InChI=1S/C21H24N2O3S/c1-25-15-3-4-19-17(8-15)21(27-12-13-5-6-22-10-13)18-9-16(26-2)7-14(11-24)20(18)23-19/h3-4,7-9,13,22,24H,5-6,10-12H2,1-2H3/t13-/m1/s1
Release date: 2021-12-01
Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase (PDB entry 6FNL)
Macromolecule: Ephrin type-B receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 297 residues
Sequence: GMDPNEAVREFAKEIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTLKGGYTERQRREFLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLNDGQFTVIQLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDFGLSRFLEENSSDPTETSSLGGKIPIRWTAPEAIAFRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPPDCPTSLHQLMLDCWQKDRNARPRFPQIVSALDKMIRNPASLKIVARENG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.269
R work: 0.1965
R free: 0.2135
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 25 % PEG5000 MME, 15 % Glycerol, 0.1 M TRIS pH7.5
Matthews coefficient: 2.1
Solvent content (%): 41.5
Release date: 2018-08-08
Crystal structure of human PTPN2 with inhibitor ABBV-CLS-484 (PDB entry 7UAD)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 324 residues
Sequence: MAMPTTIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKEDLSPAFDHSPNKIMTEKYNHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.044
R work: 0.2033
R free: 0.2452
Average B factor: 51.37
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 25% PEG3350, 0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5
Matthews coefficient: 2.7
Solvent content (%): 54.42
Ligand: 5-{(7R)-1-fluoro-3-hydroxy-7-[(3-methylbutyl)amino]-5,6,7,8-tetrahydronaphthalen-2-yl}-1lambda~6~,2,5-thiadiazolidine-1,1,3-trione (M5R)
Ligand formula: C17 H24 F N3 O4 S
Ligand molecular weight: 385.454
Ligand SMILES: CC(C)CCNC1CCc2cc(c(c(c2C1)F)N3CC(=O)NS3(=O)=O)O
Ligand InChI: InChI=1S/C17H24FN3O4S/c1-10(2)5-6-19-12-4-3-11-7-14(22)17(16(18)13(11)8-12)21-9-15(23)20-26(21,24)25/h7,10,12,19,22H,3-6,8-9H2,1-2H3,(H,20,23)/t12-/m1/s1
Release date: 2023-07-26
Crystal structure of the catalytic domain of human PARP1 in complex with olaparib (PDB entry 7AAD)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 352 residues
Sequence: GSKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.223
R free: 0.254
Average B factor: 39.33
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 2.5 M ammonium sulfate, 0.1 M Tris pH 8.5
Matthews coefficient: 2.26
Solvent content (%): 45.69
Ligand: 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one (09L)
Ligand formula: C24 H23 F N4 O3
Ligand molecular weight: 434.463
Ligand SMILES: c1ccc2c(c1)C(=NNC2=O)Cc3ccc(c(c3)C(=O)N4CCN(CC4)C(=O)C5CC5)F
Ligand InChI: InChI=1S/C24H23FN4O3/c25-20-8-5-15(14-21-17-3-1-2-4-18(17)22(30)27-26-21)13-19(20)24(32)29-11-9-28(10-12-29)23(31)16-6-7-16/h1-5,8,13,16H,6-7,9-12,14H2,(H,27,30)
Release date: 2021-01-13
Crystal structure of human chitotriosidase-1 catalytic domain at 1.0 A resolution (PDB entry 4WJX)
Macromolecule: Chitotriosidase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.14
Sequence length: 377 residues
Sequence: AKLVCYFTNWAQYRQGEARFLPKDLDPSLCTHLIYAFAGMTNHQLSTTEWNDETLYQEFNGLKKMNPKLKTLLAIGGWNFGTQKFTDMVATANNRQTFVNSAIRFLRKYSFDGLDLDWEYPGSQGSPAVDKERFTTLVQDLANAFQQEAQTSGKERLLLSAAVPAGQTYVDAGYEVDKIAQNLDFVNLMAYDFHGSWEKVTGHNSPLYKRQEESGAAASLNVDAAVQQWLQKGTPASKLILGMPTYGRSFTLASSSDTRVGAPATGSGTPGPFTKEGGMLAYYEVCSWKGATKQRIQDQKVPYIFRDNQWVGFDDVESFKTKVSYLKQKGLGGAMVWALDLDDFAGFSCNQGRYPLIQTLRQELSLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1
R work: 0.1352
R free: 0.1475
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 25 % (w/v) polyethylene glycol (PEG) 3350, 0.2 M potassium sodium tartrate (PST) at pH 7.2
Matthews coefficient: 2.23
Solvent content (%): 44.79
Ligand: L(+)-TARTARIC ACID (TLA)
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-/m1/s1
Release date: 2015-07-08
DPP1 in complex with inhibitor (PDB entry 6RNI)
Macromolecule: Dipeptidyl peptidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.14.1
Sequence length: 119 residues
Sequence: DTPANCTYLDLLGTWVFQVGSSGSQRDVNCSVMGPQEKKVVVYLQKLDTAYDDLGNSGHFTIIYNQGFEIVLNDYKWFAFFKYKEEGSKVTTYCNETMTGWVHDVLGRNWACFTGKKVG
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.54
R work: 0.196
R free: 0.209
Average B factor: 22.05
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, 0.2 M Ammonium sulphate, 0.1 M Sodium acetate
Matthews coefficient: 2.79
Solvent content (%): 55.89
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: 2019-08-28
Crystal structure of TNIK-thiopeptide TP1 complex (PDB entry 7XZQ)
Macromolecule: TRAF2 and NCK-interacting protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 306 residues
Sequence: GPDEIDLSALRDPAGIFELVELVGNGTYGQVYKGRHVKTGQLAAIKVMDVTGDEEEEIKQEINMLKKYSHHRNIATYYGAFIKKNPPGMDDQLWLVMEFCGAGSVTDLIKNTKGNTLKEEWIAYICREILRGLSHLHQHKVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATYDFKSDLWSLGITAIEMAEGAPPLCDMHPMRALFLIPRNPAPRLKSKKWSKKFQSFIESCLVKNHSQRPATEQLMKHPFIRDQPNERQVRIQLKDHIDRTKKKRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.196
R free: 0.255
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: Hepes-Na, NaCl, 1,4-butanediol
Matthews coefficient: 2.73
Solvent content (%): 54.96
Ligand: 1,4-BUTANEDIOL (BU1)
Ligand formula: C4 H10 O2
Ligand molecular weight: 90.121
Ligand SMILES: C(CCO)CO
Ligand InChI: InChI=1S/C4H10O2/c5-3-1-2-4-6/h5-6H,1-4H2
Release date: 2022-10-26
Crystal structure of FTO-IN115 (PDB entry 5DAB)
Macromolecule: Alpha-ketoglutarate-dependent dioxygenase FTO
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: LESHMTPKDDEFYQQWQLKYPKLILREASSVSEELHKEVQEAFLTLHKHGCLFRDLVRIQGKDLLTPVSRILIGNPGCTYKYLNTRLFTVPWPVKGSNIKHTEAEIAAACETFLKLNDYLQIETIQALEELAAKEKANEDAVPLCMSADFPRVGMGSSYNGDVEVDIKSRAAYNVTLLNFMDPQKMPYLKEEPYFGMGKMAVSWHHDENLVDRSAVAVYSYSCEGPEEESEDDSHLEGRDPDIWHVGFKISWDIETPGLAIPLHQGDCYFMLDDLNATHQHCVLAGSQPRFSSTHRVAECSTGTLDYILQRCQLALQNVCDDVDNDDVSLKSFEPAVLKQGEEIHNEVEFEWLRQFWFQGNRYRKCTDWWCQPMAQLEALWKKMEGVTNAVLHEVKREGLPVEQRNEILTAILASLTARQNLRREWHARCQSRIARTLPADQKPECRPYWEKDDASMPLPFDLTDIVSELRGQLLEAKP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.21
R free: 0.2409
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 10%(w/v) polyethylene glycol (PEG) 3350, 0.1 M trisodium citrate dehydrate, 3.0 mM N-oxalylglycine (NOG)
Matthews coefficient: 2.92
Solvent content (%): 61.65
Ligand: N-(5-chloro-2,4-dihydroxyphenyl)-1-phenylcyclobutanecarboxamide (58W)
Ligand formula: C17 H16 Cl N O3
Ligand molecular weight: 317.767
Ligand SMILES: c1ccc(cc1)C2(CCC2)C(=O)Nc3cc(c(cc3O)O)Cl
Ligand InChI: InChI=1S/C17H16ClNO3/c18-12-9-13(15(21)10-14(12)20)19-16(22)17(7-4-8-17)11-5-2-1-3-6-11/h1-3,5-6,9-10,20-21H,4,7-8H2,(H,19,22)
Release date: 2016-08-24
Crystal structure of JNK3 in complex with a pyridinylimidazole inhibitor (PDB entry 6EKD)
Macromolecule: Mitogen-activated protein kinase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 367 residues
Sequence: GGSMSKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2056
R free: 0.25902
Average B factor: 52.355
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Bis Tris pH 5.5, 200 mM NaCl, 29% PEG 3350, 1 mM AMP-PCP, 0.4 mM Zwittergent 3-14, 10% Ethylene glycol
Matthews coefficient: 2.07
Solvent content (%): 40.67
Ligand: BETA-MERCAPTOETHANOL (BME)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: C(CS)O
Ligand InChI: InChI=1S/C2H6OS/c3-1-2-4/h3-4H,1-2H2
Release date: 2018-08-08
Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail (PDB entry 6WW3)
Macromolecule: SUMO1 linked HERC2 ZZ domain (Small ubiquitin-related modifier 1,E3 ubiquitin-protein ligase HERC2)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 60 residues
Sequence: SDQEAKIHPGVTCDGCQMFPINGSRFKCRNCDDFDFCETCFKTKKHNTRHTFGRINEPGQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.096
R work: 0.1847
R free: 0.2268
Average B factor: 14.5705
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.2 M ammonium chloride, 0.1 M Tris, pH 8.0 and 20% PEG 6000
Matthews coefficient: 1.99
Solvent content (%): 38.08
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2020-08-05
The Crystal Structure of Human Kynurenine Aminotransferase II, PLP-bound form, at 1.83 A (PDB entry 5EUN)
Macromolecule: Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.6.1.39
Sequence length: 425 residues
Sequence: MNYARFITAASAARNPSPIRTMTDILSRGPKSMISLAGGLPNPNMFPFKTAVITVENGKTIQFGEEMMKRALQYSPSAGIPELLSWLKQLQIKLHNPPTIHYPPSQGQMDLCVTSGSQQGLCKVFEMIINPGDNVLLDEPAYSGTLQSLHPLGCNIINVASDESGIVPDSLRDILSRWKPEDAKNPQKNTPKFLYTVPNGNNPTGNSLTSERKKEIYELARKYDFLIIEDDPYYFLQFNKFRVPTFLSMDVDGRVIRADSFSKIISSGLRIGFLTGPKPLIERVILHIQVSTLHPSTFNQLMISQLLHEWGEEGFMAHVDRVIDFYSNQKDAILAAADKWLTGLAEWHVPAAGMFLWIKVKGINDVKELIEEKAVKMGVLMLPGNAFYVDSSAPSPYLRASFSSASPEQMDVAFQVLAQLIKESL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.825
R work: 0.1733
R free: 0.199
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Protein (1 uL) at a concentration of 7 mg/mL were mixed with an equal volume of a reservoir solution containing 200 mM NaCl, 0.1M NaCitrate pH 5.6, 24% PEG4K and equilibrated against 1 mL of a reservoir solution at 293 K.
Matthews coefficient: 2.4
Solvent content (%): 48.1
Release date: 2015-12-16