satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of KDM4D with tetrazolylhydrazide ligand NR073 (PDB entry 6H10)
Macromolecule: Lysine-specific demethylase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 342 residues
Sequence: METMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQDR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.104
R work: 0.1213
R free: 0.1331
Average B factor: 17.4623
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 100mM HEPES, 180mM ammonium sulphate, 24% PEG 3350
Matthews coefficient: 2.52
Solvent content (%): 51.28
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: 2020-01-29
Co- Carbonic Anhydrase II pH 11.0 20 atm CO2 (PDB entry 6LV4)
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): 1.2
R work: 0.1125
R free: 0.1394
Average B factor: 13.542
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 11
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.1
Solvent content (%): 41.51
Ligand: CARBON DIOXIDE (CO2)
Ligand formula: C O2
Ligand molecular weight: 44.01
Ligand SMILES: C(=O)=O
Ligand InChI: InChI=1S/CO2/c2-1-3
Release date: 2020-08-19
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH2, beta, gamma dTTP analogue (PDB entry 6CTP)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 16 residues
Sequence: CCGACAGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2247
R free: 0.2901
Average B factor: 46.017
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.25
Solvent content (%): 45.41
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: 2018-06-20
Crystal structure of human DNA polymerase eta incorporating 5F-dUTP across HX (PDB entry 8SKI)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 432 residues
Sequence: MATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.163
R work: 0.1996
R free: 0.2493
Average B factor: 42.81
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, pH 6.5, 20% PEG2000 MME, 5 mM calcium chloride
Matthews coefficient: 2.09
Solvent content (%): 41.15
Ligand: 2'-deoxy-5-fluorouridine 5'-(tetrahydrogen triphosphate) (B7P)
Ligand formula: C9 H14 F N2 O14 P3
Ligand molecular weight: 486.132
Ligand SMILES: C1C(C(OC1N2C=C(C(=O)NC2=O)F)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C9H14FN2O14P3/c10-4-2-12(9(15)11-8(4)14)7-1-5(13)6(24-7)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h2,5-7,13H,1,3H2,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t5-,6+,7+/m0/s1
Release date: 2023-09-20
Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(5-chloro-2-(hydroxymethyl)benzy l)pyrrolidine-2-carboxamide (PDB entry 5LCE)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.39
R work: 0.14
R free: 0.1678
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM Sodium dihydrogen phosphate ph 7.5, 
350 mM NaCl
27% PEG 8000
Matthews coefficient: 2.5
Solvent content (%): 50.2
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: 2017-07-26
Crystal structure of human DHODH in complex with BAY 2402234 (PDB entry 6QU7)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 366 residues
Sequence: ATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.15152
R free: 0.17324
Average B factor: 23.278
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.3 M NH4SO4, 0.1 M Na-acetate, 30% Glycerol
Matthews coefficient: 3.67
Solvent content (%): 66.45
Ligand: OROTIC ACID (ORO)
Ligand formula: C5 H4 N2 O4
Ligand molecular weight: 156.096
Ligand SMILES: C1=C(NC(=O)NC1=O)C(=O)O
Ligand InChI: InChI=1S/C5H4N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h1H,(H,9,10)(H2,6,7,8,11)
Release date: 2019-06-05
PKMYT1_Cocrystal_Cpd 4 (PDB entry 8WJY)
Macromolecule: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 311 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMHQLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.17193
R free: 0.21718
Average B factor: 28.242
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: SM5-E1+30%Gly
Matthews coefficient: 2.12
Solvent content (%): 41.98
Ligand: [6-azanyl-5-(2,6-dimethyl-3-oxidanyl-phenyl)-2,3-dimethyl-pyrrolo[2,3-b]pyrazin-7-yl]-(6,7-dihydro-4~{H}-pyrazolo[1,5-a]pyrazin-5-yl)methanone (W9X)
Ligand formula: C23 H25 N7 O2
Ligand molecular weight: 431.49
Ligand SMILES: Cc1ccc(c(c1n2c(c(c3c2nc(c(n3)C)C)C(=O)N4CCn5c(ccn5)C4)N)C)O
Ligand InChI: InChI=1S/C23H25N7O2/c1-12-5-6-17(31)13(2)20(12)30-21(24)18(19-22(30)27-15(4)14(3)26-19)23(32)28-9-10-29-16(11-28)7-8-25-29/h5-8,31H,9-11,24H2,1-4H3
Release date: 2023-11-22
Fragment-based discovery of 6-arylindazole JAK inhibitors (PDB entry 5L3A)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 295 residues
Sequence: GSDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEFFKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.2333
R free: 0.27657
Average B factor: 40.346
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2.1M Na Malonate pH 6.0/6.5, 0.1M glycine pH 8.2
Matthews coefficient: 3.16
Solvent content (%): 60
Ligand: ~{N}-(1~{H}-indazol-4-yl)methanesulfonamide (6DP)
Ligand formula: C8 H9 N3 O2 S
Ligand molecular weight: 211.241
Ligand SMILES: CS(=O)(=O)Nc1cccc2c1cn[nH]2
Ligand InChI: InChI=1S/C8H9N3O2S/c1-14(12,13)11-8-4-2-3-7-6(8)5-9-10-7/h2-5,11H,1H3,(H,9,10)
Release date: 2016-04-27
CDK2/cyclin A2 in complex with open-ring 5-nitrosopyrimidine inhibitor LC436 (PDB entry 6RIJ)
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): 2.2
R work: 0.2035
R free: 0.2376
Average B factor: 48.065
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 10% w/v PEG 4000, 20% v/v glycerol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, and 0.1 M MES/imidazole pH 6.5
Matthews coefficient: 3.42
Solvent content (%): 64.08
Ligand: 4-[[[5-nitroso-2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-6-(propan-2-ylamino)pyrimidin-4-yl]amino]methyl]phenol (K4W)
Ligand formula: C18 H26 N6 O3
Ligand molecular weight: 374.437
Ligand SMILES: CCC(CO)Nc1nc(c(c(n1)NC(C)C)N=O)NCc2ccc(cc2)O
Ligand InChI: InChI=1S/C18H26N6O3/c1-4-13(10-25)21-18-22-16(15(24-27)17(23-18)20-11(2)3)19-9-12-5-7-14(26)8-6-12/h5-8,11,13,25-26H,4,9-10H2,1-3H3,(H3,19,20,21,22,23)/t13-/m1/s1
Release date: 2020-07-22
Crystal structure of CLK3 in complex with macrocycle ODS2002941 (PDB entry 6Z51)
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): 1.92
R work: 0.162
R free: 0.2085
Average B factor: 20.177
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 24% PEG 3350, 0.2M potassium/sodium phosphate, 10% ethylene glycol
Matthews coefficient: 2.45
Solvent content (%): 49.89
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: 2020-06-03
Crystal structure of the methyl-CpG-binding domain of SETDB2 in complex with the cysteine-rich domain of C11orf46 protein (PDB entry 8HFP)
Macromolecule: ARL14 effector protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 77 residues
Sequence: GPQVIPAKSKVYDSQGLLIFSGMDLCDCLDEDCLGCFYACPACGSTKCGAECRCDRKWLYEQIEIEGGEIIHNKHAG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.18615
R free: 0.22662
Average B factor: 34.278
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 2.0 M ammonium sulfate
0.1 M Bis-Tris, pH 5.5
Matthews coefficient: 1.97
Solvent content (%): 37.5
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: 2023-11-22
Crystal structure of pseudokinase CASK in complex with compound 7 (PDB entry 7OAJ)
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): 1.93
R work: 0.1946
R free: 0.2238
Average B factor: 34.554
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 9% medium molecular weight PED Smears, 0.1 M magnesium acetate, 10% ethylene glycol, 0.1 M MES, pH 6.5
Matthews coefficient: 2.21
Solvent content (%): 44.39
Ligand: 4-(cyclopentylamino)-2-[(3,4-dichlorophenyl)methylamino]-N-[3-(2-oxidanylidenepyrrolidin-1-yl)propyl]pyrimidine-5-carboxamide (V6E)
Ligand formula: C24 H30 Cl2 N6 O2
Ligand molecular weight: 505.44
Ligand SMILES: c1cc(c(cc1CNc2ncc(c(n2)NC3CCCC3)C(=O)NCCCN4CCCC4=O)Cl)Cl
Ligand InChI: InChI=1S/C24H30Cl2N6O2/c25-19-9-8-16(13-20(19)26)14-28-24-29-15-18(22(31-24)30-17-5-1-2-6-17)23(34)27-10-4-12-32-11-3-7-21(32)33/h8-9,13,15,17H,1-7,10-12,14H2,(H,27,34)(H2,28,29,30,31)
Release date: 2021-05-19
Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Niraparib (MK-4827) (PDB entry 8HLQ)
Macromolecule: Poly [ADP-ribose] polymerase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 353 residues
Sequence: GPESQLDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKSERQGLEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.226
R free: 0.2816
Average B factor: 58.59
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 25% PEG-3350, 0.1 M Tris-HCl pH 8.5
Matthews coefficient: 2.19
Solvent content (%): 43.72
Ligand: 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide (3JD)
Ligand formula: C19 H20 N4 O
Ligand molecular weight: 320.388
Ligand SMILES: c1cc2cn(nc2c(c1)C(=O)N)c3ccc(cc3)C4CCCNC4
Ligand InChI: InChI=1S/C19H20N4O/c20-19(24)17-5-1-3-15-12-23(22-18(15)17)16-8-6-13(7-9-16)14-4-2-10-21-11-14/h1,3,5-9,12,14,21H,2,4,10-11H2,(H2,20,24)/t14-/m1/s1
Release date: 2024-05-01
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 19 (PDB entry 8BOC)
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): 1.9
R work: 0.246
R free: 0.2856
Average B factor: 46.98
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 37,5 % MPD_PEG 1000_PEG 3350, 175 mM Morpheus Carboxylic acids Mix, 100 mM Sodium citrate tribasic dihydrate, 100 mM Morpheus Buffer System 3 pH 8.5
Matthews coefficient: 2.17
Solvent content (%): 43.26
Ligand: ~{N}-[3,5-bis(trifluoromethyl)phenyl]-4-methyl-3-[(1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]benzamide (QUF)
Ligand formula: C27 H19 F6 N7 O
Ligand molecular weight: 571.476
Ligand SMILES: Cc1ccc(cc1Nc2c3cnn(c3nc(n2)c4cccnc4)C)C(=O)Nc5cc(cc(c5)C(F)(F)F)C(F)(F)F
Ligand InChI: InChI=1S/C27H19F6N7O/c1-14-5-6-15(25(41)36-19-10-17(26(28,29)30)9-18(11-19)27(31,32)33)8-21(14)37-23-20-13-35-40(2)24(20)39-22(38-23)16-4-3-7-34-12-16/h3-13H,1-2H3,(H,36,41)(H,37,38,39)
Release date: 2023-11-29
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1148165337 (PDB entry 7G87)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.053
R work: 0.1906
R free: 0.2414
Average B factor: 36.79
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.55
Solvent content (%): 51.75
Ligand: 2-(1H-indazol-1-yl)-N,N-dimethylacetamide (YG5)
Ligand formula: C11 H13 N3 O
Ligand molecular weight: 203.24
Ligand SMILES: CN(C)C(=O)Cn1c2ccccc2cn1
Ligand InChI: InChI=1S/C11H13N3O/c1-13(2)11(15)8-14-10-6-4-3-5-9(10)7-12-14/h3-7H,8H2,1-2H3
Release date: 2023-07-12
Crystal structure of FGFR4 kinase domain in complex with a covalent inhibitor (PDB entry 6IUO)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 322 residues
Sequence: MGSSHHHHHHSSGLLAGLVSLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDEVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.186
R free: 0.232
Average B factor: 36.63
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M HEPES pH7.5, 1.3 M (NH4)2SO4
Matthews coefficient: 2.66
Solvent content (%): 53.81
Ligand: N-({4-[4-amino-3-(3,5-dimethyl-1-benzofuran-2-yl)-7-oxo-6,7-dihydro-2H-pyrazolo[3,4-d]pyridazin-2-yl]phenyl}methyl)prop-2-enamide (AWX)
Ligand formula: C25 H22 N6 O3
Ligand molecular weight: 454.481
Ligand SMILES: Cc1ccc2c(c1)c(c(o2)c3c4c(nn3c5ccc(cc5)CNC(=O)C=C)C(=O)NN=C4N)C
Ligand InChI: InChI=1S/C25H22N6O3/c1-4-19(32)27-12-15-6-8-16(9-7-15)31-22(20-21(30-31)25(33)29-28-24(20)26)23-14(3)17-11-13(2)5-10-18(17)34-23/h4-11H,1,12H2,2-3H3,(H2,26,28)(H,27,32)(H,29,33)
Release date: 2019-10-23
Coagulation factor XI protease domain in complex with active site inhibitor (PDB entry 6TS5)
Macromolecule: Coagulation factor XI
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 238 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.1875
R free: 0.2075
Average B factor: 18.48
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH5.5, 25% w/v Polyethylene glycol 3350
Protein at 18mg/ml in 50mM Tris/HCl pH7.4 100mM NaCl
Matthews coefficient: 2.27
Solvent content (%): 45.84
Ligand: 2-[2-[3-[(3~{S})-3-azanyl-2,3-dihydro-1-benzofuran-5-yl]-5-propan-2-yl-phenyl]ethoxy]-3-methoxy-benzoic acid (NW2)
Ligand formula: C27 H29 N O5
Ligand molecular weight: 447.523
Ligand SMILES: CC(C)c1cc(cc(c1)c2ccc3c(c2)C(CO3)N)CCOc4c(cccc4OC)C(=O)O
Ligand InChI: InChI=1S/C27H29NO5/c1-16(2)19-11-17(9-10-32-26-21(27(29)30)5-4-6-25(26)31-3)12-20(13-19)18-7-8-24-22(14-18)23(28)15-33-24/h4-8,11-14,16,23H,9-10,15,28H2,1-3H3,(H,29,30)/t23-/m1/s1
Release date: 2020-07-08
MST3 IN COMPLEX WITH 2-(4,6-Diamino-1,3,5-triazin-2-yl)phenol (PDB entry 4QNA)
Macromolecule: SERINE/THREONINE-PROTEIN KINASE 24
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 310 residues
Sequence: GPLGSEFMAHSPVQSGLPGMQNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHSEKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKVLFLIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDRYKRWKAEQSHDDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.849
R work: 0.1801
R free: 0.2148
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 12.5 mg/mL MST3, 1 mM 2-(4,6- Diamino-1,3,5-triazin-2-yl)phenol, 25 mM TRIS, PH 8.0, 50 MM HEPES, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 2.07
Solvent content (%): 40.66
Ligand: 2-(4,6-diamino-1,3,5-triazin-2-yl)phenol (X11)
Ligand formula: C9 H9 N5 O
Ligand molecular weight: 203.201
Ligand SMILES: c1ccc(c(c1)c2nc(nc(n2)N)N)O
Ligand InChI: InChI=1S/C9H9N5O/c10-8-12-7(13-9(11)14-8)5-3-1-2-4-6(5)15/h1-4,15H,(H4,10,11,12,13,14)
Release date: 2015-07-01
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000899b (PDB entry 7GTB)
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): 1.86
R work: 0.2085
R free: 0.2397
Average B factor: 38.883
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: 3.38
Solvent content (%): 63.64
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