satarupa22/MacromolecularLigandDB huggingface dataset:
Bruton's tyrosine kinase in complex with N-[(2R)-1-[(3R)-3-(methylcarbamoyl)-1H,2H,3H,4H,9H-pyrido[3,4-b]indol-2-yl]-3-(3-methylphenyl)-1-oxopropan-2-yl]-1H-indazole-5-carboxamide (PDB entry 8U2E)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 270 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1908
R free: 0.2377
Average B factor: 23.28
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 30% EDO_P8K, 0.03M NaN03, 0.03M Na2HPO4 0.03M (NH4)2SO4, 0.05M Imidazole, 0.05M MES pH 6.5
Matthews coefficient: 2.5
Solvent content (%): 50.82
Ligand: (2S)-6-fluoro-5-[(3S)-3-(3-methyl-2-oxoimidazolidin-1-yl)piperidin-1-yl]-2-(4-methylpiperazine-1-carbonyl)-2,3,4,9-tetrahydro-1H-carbazole-8-carboxamide (UP9)
Ligand formula: C28 H38 F N7 O3
Ligand molecular weight: 539.645
Ligand SMILES: CN1CCN(CC1)C(=O)C2CCc3c([nH]c4c3c(c(cc4C(=O)N)F)N5CCCC(C5)N6CCN(C6=O)C)C2
Ligand InChI: InChI=1S/C28H38FN7O3/c1-32-8-11-34(12-9-32)27(38)17-5-6-19-22(14-17)31-24-20(26(30)37)15-21(29)25(23(19)24)35-7-3-4-18(16-35)36-13-10-33(2)28(36)39/h15,17-18,31H,3-14,16H2,1-2H3,(H2,30,37)/t17-,18-/m0/s1
Release date: 2024-01-31
Alternative model of the MAGE-G1 NSE-1 complex (PDB entry 5HVQ)
Macromolecule: Melanoma-associated antigen G1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 217 residues
Sequence: GPRSQKQLELKVSELVQFLLIKDQKKIPIKRADILKHVIGDYKDIFPDLFKRAAERLQYVFGYKLVELEPKSNTYILINTLEPVEEDAEMRGDQGTPTTGLLMIVLGLIFMKGNTLKETEAWDFLRRLGVYPTKKHLIFGDPKKLITEDFVRQRYLEYRRIPHTDPVDYEFQWGPRTNLELSKMKVLKFVAKVHNQDPKDWPAQYCEALADEENRAR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.923
R work: 0.2367
R free: 0.2678
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: As for entry 3nw0
Matthews coefficient: 3.24
Solvent content (%): 62.08
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
Irak4-inhibitor co-structure (PDB entry 4ZTL)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: VSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.39
R work: 0.2245
R free: 0.2508
Average B factor: 76.16
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 289
Crystal growth procedure: 1.80 to 2.0 M Sodium Malonate, 0.2 M Sodium Acetate, 25 mM Hexamminecobalt(III)chloride, 0.05%w/v Pluronic-F-68
Matthews coefficient: 2.65
Solvent content (%): 53.65
Ligand: (1R,2S,3R,5R)-3-{[5-(1,3-benzothiazol-2-yl)-2-(propylamino)pyrimidin-4-yl]amino}-5-(hydroxymethyl)cyclopentane-1,2-diol (4S1)
Ligand formula: C20 H25 N5 O3 S
Ligand molecular weight: 415.509
Ligand SMILES: CCCNc1ncc(c(n1)NC2CC(C(C2O)O)CO)c3nc4ccccc4s3
Ligand InChI: InChI=1S/C20H25N5O3S/c1-2-7-21-20-22-9-12(19-24-13-5-3-4-6-15(13)29-19)18(25-20)23-14-8-11(10-26)16(27)17(14)28/h3-6,9,11,14,16-17,26-28H,2,7-8,10H2,1H3,(H2,21,22,23,25)/t11-,14-,16-,17+/m1/s1
Release date: 2015-09-02
Crystal structure of oncogenic RhoA mutant G14V complexed with GDP (PDB entry 6V6V)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 183 residues
Sequence: GSMAAIRKKLVIVGDVACGKTCLLIVNSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.2018
R free: 0.2234
Average B factor: 29.248
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 277
Crystal growth procedure: 20-24% PEG8K, 15% Dioxane, 0.1M Tris pH8.0
Matthews coefficient: 2.31
Solvent content (%): 46.64
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2020-12-23
Complement factor B protease domain in complex with the reversible inhibitor 4-((2S,4S)-4-ethoxy-1-((5-methoxy-7-methyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid (PDB entry 6RAV)
Macromolecule: Complement factor B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.47
Sequence length: 291 residues
Sequence: SLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1952
R free: 0.2267
Average B factor: 31.753
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 24 % (w/v) PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris (pH 5.5), 2mM inhibitor
Matthews coefficient: 2.54
Solvent content (%): 51.59
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: 2019-04-17
EGFR(T790M/V948R) in complex with the allosteric inhibitor FRF-06-057 (PDB entry 8TO4)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 328 residues
Sequence: SGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.99
R work: 0.1711
R free: 0.231
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG-3350, Bis-Tris 0.1 M
Matthews coefficient: 2.11
Solvent content (%): 41.64
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2024-08-28
Crystal Structure of KDM4D with GF026 ligand (PDB entry 6F5Q)
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): 1.43
R work: 0.1434
R free: 0.1736
Average B factor: 22.2506
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 100mM HEPES, 180mM ammonium sulphate, 24% PEG 3350
Matthews coefficient: 2.61
Solvent content (%): 52.9
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: 2018-12-12
Crystal structure of CK2alpha with 2-hydroxy-5-methylbenzoic acid and N-(3-(3-chloro-4-(phenyl)benzylamino)propyl)acetamide bound (PDB entry 5CU0)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.18
R work: 0.2044
R free: 0.236
Average B factor: 48.36
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 107mM Mes pH 6.5, 29% glycerol ethoxylate, 1 M ammonium acetate
Matthews coefficient: 2.23
Solvent content (%): 44.77
Ligand: N-(3-{[(2-chlorobiphenyl-4-yl)methyl]amino}propyl)acetamide (54R)
Ligand formula: C18 H21 Cl N2 O
Ligand molecular weight: 316.825
Ligand SMILES: CC(=O)NCCCNCc1ccc(c(c1)Cl)c2ccccc2
Ligand InChI: InChI=1S/C18H21ClN2O/c1-14(22)21-11-5-10-20-13-15-8-9-17(18(19)12-15)16-6-3-2-4-7-16/h2-4,6-9,12,20H,5,10-11,13H2,1H3,(H,21,22)
Release date: 2016-11-30
Crystal structure of WNK1 in complex with Mn2+AMPPNP and WNK476 (PDB entry 5TF9)
Macromolecule: Serine/threonine-protein kinase WNK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 279 residues
Sequence: GELETKAVGMSNDGRFLKFDIEIGRGSFKTVYKGLDTETTVEVAWCELQDRKLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWESTVKGKKCIVLVTELMTSGTLKTYLKRFKVMKIKVLRSWCRQILKGLQFLHTRTPPIIHRDLKCDNIFITGPTGSVKIGDLGLATLKRADFAKSVIGTPEFMAPEMYAAAYDESVDVYAFGMCMLEMATSEYPYSECQNAAQIYRRVTSGVKPASFDKVAIPEVKEIIEGCIRQNKDERYSIKDLLNHAFFQEET
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1949
R free: 0.2658
Average B factor: 46.0336
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM HEPES, pH 7.5, 200 mM calcium acetate, 22% PEG3350
Matthews coefficient: 2.12
Solvent content (%): 41.95
Ligand: {2-[(4-chlorophenyl)methoxy]phenyl}{5-[2-(methylamino)-1,3-thiazol-4-yl]-2,3-dihydro-1H-indol-1-yl}methanone (7AV)
Ligand formula: C26 H22 Cl N3 O2 S
Ligand molecular weight: 475.99
Ligand SMILES: CNc1nc(cs1)c2ccc3c(c2)CCN3C(=O)c4ccccc4OCc5ccc(cc5)Cl
Ligand InChI: InChI=1S/C26H22ClN3O2S/c1-28-26-29-22(16-33-26)18-8-11-23-19(14-18)12-13-30(23)25(31)21-4-2-3-5-24(21)32-15-17-6-9-20(27)10-7-17/h2-11,14,16H,12-13,15H2,1H3,(H,28,29)
Release date: 2016-10-19
Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the ATP-competitive inhibitor 5,6,7-tribromo-1H-triazolo[4,5-b]pyridine (PDB entry 7A22)
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): 1.01
R work: 0.1379
R free: 0.166
Average B factor: 17.17
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser)/inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the inhibitor 5,6,7-tribromo-1H-triazolo[4,5-b]pyridine by extensive crystal soaking.
Matthews coefficient: 2.63
Solvent content (%): 53.31
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: 2020-12-09
Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor (PDB entry 5A8Z)
Macromolecule: Neutrophil elastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.37
Sequence length: 218 residues
Sequence: IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.18993
R free: 0.23644
Average B factor: 22.703
Matthews coefficient: 2.32
Solvent content (%): 47.02
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: 2016-08-03
Crystal Structure of Anaplastic Lymphoma Kinase (ALK) in complex with 5a (PDB entry 5IUG)
Macromolecule: ALK tyrosine kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 327 residues
Sequence: RTSTIMTDYNPNYSFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVEEEEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.1829
R free: 0.2112
Average B factor: 29.3488
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.6
Crystallization temperature (K): 277
Crystal growth procedure: 18% PEG2000 MME, 0.1 M Tris-HCl pH 8.6
Matthews coefficient: 2.04
Solvent content (%): 39.81
Ligand: N-[3-(4-{[(5-tert-butyl-1,2-oxazol-3-yl)carbamoyl]amino}-3-methylphenyl)-1H-pyrazol-5-yl]-4-[(4-methylpiperazin-1-yl)methyl]benzamide (729)
Ligand formula: C31 H38 N8 O3
Ligand molecular weight: 570.685
Ligand SMILES: Cc1cc(ccc1NC(=O)Nc2cc(on2)C(C)(C)C)c3cc([nH]n3)NC(=O)c4ccc(cc4)CN5CCN(CC5)C
Ligand InChI: InChI=1S/C31H38N8O3/c1-20-16-23(10-11-24(20)32-30(41)34-28-18-26(42-37-28)31(2,3)4)25-17-27(36-35-25)33-29(40)22-8-6-21(7-9-22)19-39-14-12-38(5)13-15-39/h6-11,16-18H,12-15,19H2,1-5H3,(H2,32,34,37,41)(H2,33,35,36,40)
Release date: 2016-05-18
CLK1 bound with CAF052 (PDB entry 7AK3)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 339 residues
Sequence: SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2108
R free: 0.2599
Average B factor: 72.692
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9.3
Crystallization temperature (K): 278
Crystal growth procedure: 23% PEG 6000, 0.1 M bicine
Matthews coefficient: 2.53
Solvent content (%): 51.3
Ligand: ~{N}-[3-fluoranyl-4-(4-methylpiperazin-1-yl)phenyl]-4-pyrazolo[1,5-b]pyridazin-3-yl-pyrimidin-2-amine (RH8)
Ligand formula: C21 H21 F N8
Ligand molecular weight: 404.443
Ligand SMILES: CN1CCN(CC1)c2ccc(cc2F)Nc3nccc(n3)c4cnn5c4cccn5
Ligand InChI: InChI=1S/C21H21FN8/c1-28-9-11-29(12-10-28)20-5-4-15(13-17(20)22)26-21-23-8-6-18(27-21)16-14-25-30-19(16)3-2-7-24-30/h2-8,13-14H,9-12H2,1H3,(H,23,26,27)
Release date: 2020-11-11
Crystal structure of human NEIL3 tandem zinc finger GRF domains (PDB entry 7JL5)
Macromolecule: Endonuclease 8-like 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 108 residues
Sequence: SNGNPDSPRCSKHNRLCILRVVGKDGENKGRQFYACPLPREAQCGFFEWADLSFPFCNHGKRSTMKTVLKIGPNNGKNFFVCPLGKEKQCNFFQWAENGPGIKIIPGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2268
R free: 0.2661
Average B factor: 51.86
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: PEG 6000
Matthews coefficient: 2.93
Solvent content (%): 57.15
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: 2020-09-09
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOOA000650a (PDB entry 5QGC)
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): 1.586
R work: 0.1834
R free: 0.2106
Average B factor: 35.7381
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.34
Solvent content (%): 63.2
Ligand: (6aS,12aR)-3-methoxy-6a,10,11,12a-tetrahydro-6H,7H,9H-[1]benzopyrano[4,3-c]pyrazolo[1,2-a]pyrazol-9-one (JQD)
Ligand formula: C14 H16 N2 O3
Ligand molecular weight: 260.288
Ligand SMILES: COc1ccc2c(c1)OCC3C2N4CCC(=O)N4C3
Ligand InChI: InChI=1S/C14H16N2O3/c1-18-10-2-3-11-12(6-10)19-8-9-7-16-13(17)4-5-15(16)14(9)11/h2-3,6,9,14H,4-5,7-8H2,1H3/t9-,14-/m1/s1
Release date: 2018-10-10
Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors (PDB entry 6P6K)
Macromolecule: Histone-lysine N-methyltransferase SMYD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 432 residues
Sequence: GSFTMEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1779
R free: 0.2142
Average B factor: 25.2112
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: apo crystals :  room temp, Linbro tray, hanging drop, 1+1, reservoir is 10% PEG 3350, 0.2M MgOAc
seeding:  scratch seed
Soaks:  2ul of 200mM compound in DMSO mixed with 2x well solution (20% PEG3350, 0.4M MgOAc)
Matthews coefficient: 2.14
Solvent content (%): 42.55
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: 2020-01-15
The human O-GlcNAc transferase in complex with a thiol-linked bisubstrate inhibitor (PDB entry 5NPR)
Macromolecule: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.255
Sequence length: 717 residues
Sequence: THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNGIDLKAFLDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIKPVE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.20497
R free: 0.23641
Average B factor: 46.58
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 295
Crystal growth procedure: Reservoir solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol

Drop solution: 1.45 M K2HPO4, 8 mM EDTA, 1% xylitol, 0.5 M (NH4)2SO4, crystal seeds

Seeds were generated from crystals grown in 1.3 M DL-Malic acid, 0.1 M Bis-Tris propane pH 6.4
Matthews coefficient: 3.33
Solvent content (%): 63
Ligand: POTASSIUM ION (K)
Ligand formula: K
Ligand molecular weight: 39.098
Ligand SMILES: [K+]
Ligand InChI: InChI=1S/K/q+1
Release date: 2018-05-16
Complement factor B in complex with (S)-5,7-Dimethyl-4-((2-phenylpiperidin-1-yl)methyl)-1H-indole (PDB entry 6T8V)
Macromolecule: Complement factor B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.47
Sequence length: 291 residues
Sequence: SLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29
R work: 0.2023
R free: 0.2539
Average B factor: 24.576
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG3350, 0.1M HEPES PH 7.5, 5 mM inhibitor
Matthews coefficient: 2.46
Solvent content (%): 50.06
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: 2020-03-04