satarupa22/MacromolecularLigandDB huggingface dataset:
Human APE1 substrate complex with an A/G mismatch adjacent the THF (PDB entry 6BOV)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 318 residues
Sequence: MPKRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQQTKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGNLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.975
R work: 0.2109
R free: 0.2423
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Matthews coefficient: 2.28
Solvent content (%): 46
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: 2018-08-15
Crystal Structure of PTPN12 Catalytic Domain (PDB entry 5HDE)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 12
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 307 residues
Sequence: GSHMASMEQVEILRKFIQRVQAMKSPDHNGEDNFARDFMRLRRLSTKYRTEKIYPTATGEKEENVKKNRYKDILPFDHSRVKLTLKTPSQDSDYINANFIKGVYGPKAYVATQGPLANTVIDFWRMIWEYNVVIIVMACREFEMGRKKCERYWPLYGEDPITFAPFKISCEDEQARTDYFIRTLLLEFQNESRRLYQFHYVNWPDHDVPSSFDSILDMISLMRKYQEHEDVPICIHCSAGCGRTGAICAIDYTWNLLKAGKIPEEFNVFNLIQEMRTQRHSAVQTKEQYELVHRAIAQLFEKQLQLY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62
R work: 0.16421
R free: 0.21265
Average B factor: 22.591
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.04M potassium phosphate, 16% w/v PEG 8000, 20% v/v glycerol
Matthews coefficient: 2.64
Solvent content (%): 53.41
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2017-01-18
Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with long-chain Fasudil-derivative (Ligand 05) (PDB entry 5LCQ)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Cricetulus griseus
EC number: 2.7.11.11
Sequence length: 353 residues
Sequence: GHMGNAAAAKKGSEQESVKEFLAKAKEEFLKKWESPSQNTAQLDHFDRIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.423
R work: 0.1411
R free: 0.171
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 277.15
Crystal growth procedure: Drop:
10 mg/ml PKA (0.240 mM)
30 mM MBT (MES/Bis-Tris Puffer pH 6.9)
1 mM DTT
0.1 mM EDTA
75 mM LiCl
0.03 mM Mega 8
0.07mM PKI (Sigma: P7739)
1.2 mM ligand solved in DMSO (50 mM Stock)

Reservoir: 18% Methanol

0.003 mL drop volume, 0.4 mL reservoir volume
Matthews coefficient: 2.15
Solvent content (%): 53.1
Ligand: ~{N}-[2-(propylamino)ethyl]isoquinoline-5-sulfonamide (6TV)
Ligand formula: C14 H19 N3 O2 S
Ligand molecular weight: 293.385
Ligand SMILES: CCCNCCNS(=O)(=O)c1cccc2c1ccnc2
Ligand InChI: InChI=1S/C14H19N3O2S/c1-2-7-15-9-10-17-20(18,19)14-5-3-4-12-11-16-8-6-13(12)14/h3-6,8,11,15,17H,2,7,9-10H2,1H3
Release date: 2018-01-17
Creating novel F1 inhibitors through fragment based lead generation and structure aided drug design (PDB entry 4CRB)
Macromolecule: COAGULATION FACTOR XI
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 238 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQAEIAEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYADSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.19
R free: 0.213
Crystallization pH: 8.5
Crystal growth procedure: 2M AMMONIUM SULFATE 0.1M TRIS-CL PH 8.5 0.2M NACL
Matthews coefficient: 2.76
Solvent content (%): 55.41
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: 2015-02-11
Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with UDP and trisaccharide GlcNAc-beta1-3Gal-beta1-4GlcNAc (PDB entry 7JHN)
Macromolecule: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.149
Sequence length: 370 residues
Sequence: MHHHHHHHHENLYFQGSKEKFWKISTPPEAYWNREQEKLNRQYNPILSMLTNQTGEAGRLSNISHLNYCEPDLRVTSVVTGFNNLPDRFKDFLLYLRCRNYSLLIDQPDKCAKKPFLLLAIKSLTPHFARRQAIRESWGQESNAGNQTVVRVFLLGQTPPEDNHPDLSDMLKFESEKHQDILMWNYRDTFFNLSLKEVLFLRWVSTSCPDTEFVFKGDDDVFVNTHHILNYLNSLSKTKAKDLFIGDVIHNAGPHRDKKLKYYIPEVVYSGLYPPYAGGGGFLYSGHLALRLYHITDQVHLYPIDDVYTGMCLQKLGLVPEKHKGFRTFDIEEKNKNNICSYVDLMLVHSRKPQEMIDIWSQLQSAHLKC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1955
R free: 0.2551
Average B factor: 38.9464
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 24% PEG1500, 20% glycerol
Matthews coefficient: 2.36
Solvent content (%): 47.98
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: 2020-11-18
Structure of phopsho-CDK2-cyclin A in complex with an ATP-competitive inhibitor (PDB entry 5LMK)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 299 residues
Sequence: SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.21156
R free: 0.24863
Average B factor: 40.22
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: ammonium sulphate; potassium chloride; sodium Hepes pH7.5
Matthews coefficient: 2.94
Solvent content (%): 58.14
Ligand: 4-[4-[3-bromanyl-7-(pyridin-3-ylmethylamino)pyrazolo[1,5-a]pyrimidin-5-yl]phenyl]benzamide (6ZK)
Ligand formula: C25 H19 Br N6 O
Ligand molecular weight: 499.362
Ligand SMILES: c1cc(cnc1)CNc2cc(nc3n2ncc3Br)c4ccc(cc4)c5ccc(cc5)C(=O)N
Ligand InChI: InChI=1S/C25H19BrN6O/c26-21-15-30-32-23(29-14-16-2-1-11-28-13-16)12-22(31-25(21)32)19-7-3-17(4-8-19)18-5-9-20(10-6-18)24(27)33/h1-13,15,29H,14H2,(H2,27,33)
Release date: 2017-01-25
Wildtype PTP1b in complex with DES5743 (PDB entry 8G69)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 298 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.16933
R free: 0.19844
Average B factor: 24.808
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.2
Crystallization temperature (K): 278
Crystal growth procedure: Reservoir solution: 50 mM MES (pH 6.2), 14% PEG6000, 50 mM MgCl2;
Protein solution: 10.3 mg/ml PTP-1B 1-298 in 25 mM Hepes pH 7.2, 150 mM NaCl, 1 mM EDTA, 2 mM DTT
Matthews coefficient: 2.27
Solvent content (%): 45.74
Ligand: 4-(5-ethyl-3-methyl-1H-pyrazol-1-yl)aniline (YXN)
Ligand formula: C12 H15 N3
Ligand molecular weight: 201.268
Ligand SMILES: CCc1cc(nn1c2ccc(cc2)N)C
Ligand InChI: InChI=1S/C12H15N3/c1-3-11-8-9(2)14-15(11)12-6-4-10(13)5-7-12/h4-8H,3,13H2,1-2H3
Release date: 2023-04-26
Crystal structure of the human CHIP TPR domain in complex with a 5mer acetylated HSP70 peptide (PDB entry 6EFK)
Macromolecule: E3 ubiquitin-protein ligase CHIP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 132 residues
Sequence: SPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQRLNFGDDIPSALRIAKKKRWNSIEERR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.2108
R free: 0.244
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.4 M CaCl2, 0.1 M HEPES (pH 7.5), 25% PEG 4000
Matthews coefficient: 2
Solvent content (%): 38.4
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2019-07-31
Structure of the catalytic domain of PARP1 in complex with olaparib (PDB entry 7KK4)
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: GSKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.217
R free: 0.266
Average B factor: 52.52
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 294
Crystal growth procedure: Salt: 0.2 M Magnesium chloride hexahydrate
Buffer: 0.1 M Tris (pH 8.50)
Precipitant: 30.0 %w/v PEG 4000
Matthews coefficient: 2.17
Solvent content (%): 43.39
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: 2021-01-06
Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with tricyclic small molecule inhibitor JBSNF-000028 (PDB entry 7ET7)
Macromolecule: Nicotinamide N-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.1
Sequence length: 281 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMESGFTSKDTYLSHFNPRDYLEKYYKFGSRHSAESQILKHLLKNLFKIFCLDGVKGDLLIDIGSGPTIYQLLSACESFKEIVVTDYSDQNLQELEKWLKAAPAAFDWSPVVTYVCDLEGNRVKGPEKEEKLRQAVKQVLKCDVTQSQPLGAVPLPPADCVLSTLCLDAACPDLPTYCRALRNLGSLLKPGGFLVIMDALKSSYYMIGEQKFSSLPLGREAVEAAVKEAGYTIEWFEVISQSYSSTMANNEGLFSLVARKLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.61
R work: 0.2231
R free: 0.2833
Average B factor: 38.825
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 295
Crystal growth procedure: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.8, 25 %(w/v) PEG 3350
Matthews coefficient: 1.99
Solvent content (%): 38.25
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2022-05-18
Crystal structure of UTX complexed with 5-carboxy-8-hydroxyquinoline (PDB entry 6FUK)
Macromolecule: Lysine-specific demethylase 6A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 531 residues
Sequence: GPGYQDPNSQIIPSMSVSIYPSSAEVLKACRNLGKNGLSNSSILLDKCPPPRPPSSPYPPLPKDKLNPPTPSIYLENKRDAFFPPLHQFCTNPNNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWHCESNRSHTTIAKYAQYQASSFQESLREENEKRSHHKDHSDSESTSSDNSGRRRKGPFKTIKFGTNIDLSDDKKWKLQLHELTKLPAFVRVVSAGNLLSHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEGYWGVLNDFCEKNNLNFLMGSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAIGWCNNIAWNVGPLTACQYKLAVERYEWNKLQSVKSIVPMVHLSWNMARNIKVSDPKLFEMIKYCLLRTLKQCQTLREALIAAGKEIIWHGRTKEEPAHYCSICEVEVFDLLFVTNESNSRKTYIVHCQDCARKTSGNLENFVVLEQYKMEDLMQVYDQFTLAPPLPSASS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1863
R free: 0.2283
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris-HCl (pH 8.5), Li2 SO4 (0.15-0.25 M), PEG 3350 (20-25% w/v)
Matthews coefficient: 2.58
Solvent content (%): 52.33
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2018-10-10
Crystal structure of CLK3 in complex with macrocycle ODS2003136 (PDB entry 6Z52)
Macromolecule: Dual specificity protein kinase CLK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 360 residues
Sequence: SMQSSKRSSRSVEDDKEGHLVCRIGDWLQERYEIVGNLGEGTFGKVVECLDHARGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVATRHYRPPEVILELGWAQPCDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSFHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.1779
R free: 0.2301
Average B factor: 22.885
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 20.0% PEG 3350, 0.20M NaI, 0.1M bis-tris propane pH 7.5, 10.0% ethylene glycol
Matthews coefficient: 3.05
Solvent content (%): 59.68
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: 2020-06-03
Peptide IILKEK in complex with human cathepsin V C25S mutant (PDB entry 7Q8J)
Macromolecule: Cathepsin L2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.43
Sequence length: 222 residues
Sequence: DLPKSVDWRKKGYVTPVKNQKQCGSSWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRPQGNQGCNGGFMARAFQYVKENGGLDSEESYPYVAVDEICKYRPENSVAQDTGFTVVAPGKEKALMKAVATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVVGYGFEGANSQNSKYWLVKNSWGPEWGSNGYVKIAKDKNNHCGIATAASYPNV
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.1928
R free: 0.2175
Average B factor: 70.05
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 77 % MPD, 23 % of 60 mM TRIS, pH 8
Matthews coefficient: 2.78
Solvent content (%): 55.78
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: 2022-11-23
Carborane nido-hexyl-sulfonamide in complex with CA II (PDB entry 6YZX)
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): 1.1
R work: 0.1431
R free: 0.1656
Average B factor: 17.428
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-H2SO4
Matthews coefficient: 2.08
Solvent content (%): 40.98
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: 2020-10-28
Crystal structure of APT1 C2S mutant bound to palmitic acid. (PDB entry 6QGQ)
Macromolecule: Acyl-protein thioesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.2
Sequence length: 234 residues
Sequence: GSRMSGNNMSTPLPAIVPAARKATAAVIFLHGLGDTGHGWAEAFAGIRSSHIKYICPHAPVRPVTLNMNVAMPSWFDIIGLSPDSQEDESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAGVTALSCWLPLRASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLVNPANVTFKTYEGMMHSSCQQEMMDVKQFIDKLLPPIDA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.601
R work: 0.1909
R free: 0.238
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 25% of of polyethylene glycol (PEG) 2000 MME, 0.3 M sodium acetate, 0.1 M sodium cacodylate pH 6.5;
Matthews coefficient: 2.51
Solvent content (%): 50.9
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: 2020-02-05
The Crystal Structure of NF-kB-inducing Kinase (NIK) from Biortus (PDB entry 8YHW)
Macromolecule: Mitogen-activated protein kinase kinase kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 351 residues
Sequence: GKFSVEEYLVHALQGSVSSGQAHSLTSLAKTWAARGSRSREPSPKTEDNEGVLLTEKLKPVDYEYREEVHWATHQLRLGRGSFGEVHRMEDKQTGFQCAVKKVRLEVFRAEELMACAGLTSPRIVPLYGAVREGPWVNIFMELLEGGSLGQLVKEQGCLPEDRALYYLGQALEGLEYLHSRRILHGDVKADNVLLSSDGSHAALCDFGHAVCLQPDGLGKSLLTGDYIPGTETHMAPEVVLGRSCDAKVDVWSSCCMMLHMLNGCHPWTQFFRGPLCLKIASEPPPVREIPPSCAPLTAQAIQEGLRKEPIHRVSAAELGGKVNRALQQVGGLKSPWRGEYKEPRHPPPNQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.194
R free: 0.2412
Average B factor: 49.624
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MMT pH9.0, 25% PEG1500
Matthews coefficient: 2.67
Solvent content (%): 53.94
Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER (AGS)
Ligand formula: C10 H16 N5 O12 P3 S
Ligand molecular weight: 523.247
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
Release date: 2024-03-13
Crystal structure of haspin in complex with disubstituted imidazo[1,2- b]pyridazine inhibitor (compound 12) (PDB entry 7AVQ)
Macromolecule: Serine/threonine-protein kinase haspin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 357 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMGECSQKGPVPFSHCLPTEKLQRCEKIGEGVFGEVFQTIADHTPVAIKIIAIEGPDLVNGSHQKTFEEILPEIIISKELSLLSGEVCNRTEGFIGLNSVHCVQGSYPPLLLKAWDHYNSTKGSANDRPDFFKDDQLFIVLEFEFGGIDLEQMRTKLSSLATAKSILHQLTASLAVAEASLRFEHRDLHWGNVLLKKTSLKKLHYTLNGKSSTIPSCGLQVSIIDYTLSRLERDGIVVFCDVSMDEDLFTGDGDYQFDIYRLMKKENNNRWGEYHPYSNVLWLHYLTDKMLKQMTFKTKCNTPAMKQIKRKIQEFHRTMLNFSSATDLLCQHSLFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1593
R free: 0.1794
Average B factor: 32.098
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 63% MPD and 0.1 M SPG, pH 6.5
Matthews coefficient: 2.9
Solvent content (%): 57.63
Ligand: (2~{R})-2-[[3-(2~{H}-indazol-5-yl)imidazo[1,2-b]pyridazin-6-yl]amino]butan-1-ol (S1Z)
Ligand formula: C17 H18 N6 O
Ligand molecular weight: 322.364
Ligand SMILES: CCC(CO)Nc1ccc2ncc(n2n1)c3ccc4c(c3)c[nH]n4
Ligand InChI: InChI=1S/C17H18N6O/c1-2-13(10-24)20-16-5-6-17-18-9-15(23(17)22-16)11-3-4-14-12(7-11)8-19-21-14/h3-9,13,24H,2,10H2,1H3,(H,19,21)(H,20,22)/t13-/m1/s1
Release date: 2020-11-18
Structure of E3 ligase NleL bound to ubiquitin (PDB entry 8ST9)
Macromolecule: E3 ubiquitin-protein ligase SopA
Type: Protein, polypeptide(L)
Source organism: Escherichia coli O157:H7 str. Sakai
EC number: 2.3.2.26
Sequence length: 179 residues
Sequence: GPNFVSGILDILISDNELKERFIEALNSNKSDYKMIADDQQRKLACVWNPFLDGWELNAQHVDMIMGSHVLKDMPLRKQAEILFCLGGVFCKYSSSDMFGTEYDSPEILRRYANGLIEQAYKTDPQVFGSVYYYNDILDRLQGRNNVFTCTAVLTDMLTEHAKESFPEIFSLYYPVAWR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2036
R free: 0.2515
Average B factor: 39.98
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 0.2 M KSCN, 0.1 M bis-tris propane pH 7.5, 20% glycerol, and 10% ethylene glycol
Matthews coefficient: 2.29
Solvent content (%): 46.19
Ligand: prop-2-en-1-amine (AYE)
Ligand formula: C3 H7 N
Ligand molecular weight: 57.094
Ligand SMILES: C=CCN
Ligand InChI: InChI=1S/C3H7N/c1-2-3-4/h2H,1,3-4H2
Release date: 2023-07-12
Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing guanidinohydantoin (Gh) (PDB entry 6LWG)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 295 residues
Sequence: MGQGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGRGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.2075
R free: 0.2537
Average B factor: 73.162
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000
Matthews coefficient: 2.75
Solvent content (%): 55.33
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: 2021-06-09