satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of EGFR 675-1022 T790M/C797S/V948R in complex with EAI045 (PDB entry 5ZWJ)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 355 residues
Sequence: GRKRTLRRLLQERELVEPLTPSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGSLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2551
R free: 0.2718
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 26% PEG 4000, 0.1 M KCl, 0.05 M Tris pH 7.5-8.0
Matthews coefficient: 2.41
Solvent content (%): 48.9
Ligand: (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)-N-(1,3-thiazol-2-yl)acetamide (9LL)
Ligand formula: C19 H14 F N3 O3 S
Ligand molecular weight: 383.396
Ligand SMILES: c1ccc2c(c1)CN(C2=O)C(c3cc(ccc3O)F)C(=O)Nc4nccs4
Ligand InChI: InChI=1S/C19H14FN3O3S/c20-12-5-6-15(24)14(9-12)16(17(25)22-19-21-7-8-27-19)23-10-11-3-1-2-4-13(11)18(23)26/h1-9,16,24H,10H2,(H,21,22,25)/t16-/m1/s1
Release date: 2018-07-25
Crystal structure of BACE complex with BMC001 (PDB entry 5QCT)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 402 residues
Sequence: GPDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.17
R free: 0.197
Average B factor: 51.54
Crystallization method: hanging drop
Crystallization pH: 5.6
Crystallization temperature (K): 292
Crystal growth procedure: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS USING 1.0M AMMONIUM PHOSPHATE, 0.1M NA CITRATE PH 5.6
AS PRECIPITANT. PROTEIN STOCK WAS BACE MUT46B BATCH X 8.3MG/ML IN 10MM TRIS-HCL PH 7. 25MM NACL, WITH A 4-FOLD EXCESS OF
BMC001 ADDED FROM A 50MM STOCK SOLUTION IN DMSO (1.4% DMSO IN DROP). CRYO-PROTECTANT WAS 20% (V/V) 1,2-PROPANEDIOL, 80%
RESERVOIR SOLUTION.
Matthews coefficient: 3.12
Solvent content (%): 60.6
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 human phosphodiesterase 10 in complex with (2-phenyl-[1,2,4]triazolo[1,5-a]pyridin-7-yl)methanol (PDB entry 5SHW)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.19
R work: 0.1784
R free: 0.2244
Average B factor: 47.649
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.62
Solvent content (%): 53.01
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: 2022-10-12
Crystal structure of the ACVR1 (ALK2) kinase in complex with a Quinazolinone based ALK2 inhibitor with a 2, 5-dimethyl core. (PDB entry 6GIP)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.1951
R free: 0.2389
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.5M ammonium sulfate, 0.1M tris pH 8.5, 4% glycerol
Matthews coefficient: 2.61
Solvent content (%): 53.1
Ligand: 2,5-dimethyl-6-quinolin-4-yl-3~{H}-quinazolin-4-one (EUN)
Ligand formula: C19 H15 N3 O
Ligand molecular weight: 301.342
Ligand SMILES: Cc1c(ccc2c1C(=O)NC(=N2)C)c3ccnc4c3cccc4
Ligand InChI: InChI=1S/C19H15N3O/c1-11-13(7-8-17-18(11)19(23)22-12(2)21-17)14-9-10-20-16-6-4-3-5-15(14)16/h3-10H,1-2H3,(H,21,22,23)
Release date: 2018-05-23
Human AURKA bound to BRD-7880 (PDB entry 6GRA)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 285 residues
Sequence: GAMESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPSNCQNKESASKQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.21005
R free: 0.26859
Average B factor: 75.206
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M potassium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% PEG 3350, 10% ethylene glycol
Matthews coefficient: 2.6
Solvent content (%): 52.76
Ligand: 1-[(2~{R},3~{S})-2-[[1,3-benzodioxol-5-ylmethyl(methyl)amino]methyl]-3-methyl-6-oxidanylidene-5-[(2~{S})-1-oxidanylpropan-2-yl]-3,4-dihydro-2~{H}-1,5-benzoxazocin-8-yl]-3-(4-methoxyphenyl)urea (F8Z)
Ligand formula: C32 H38 N4 O7
Ligand molecular weight: 590.667
Ligand SMILES: CC1CN(C(=O)c2cc(ccc2OC1CN(C)Cc3ccc4c(c3)OCO4)NC(=O)Nc5ccc(cc5)OC)C(C)CO
Ligand InChI: InChI=1S/C32H38N4O7/c1-20-15-36(21(2)18-37)31(38)26-14-24(34-32(39)33-23-6-9-25(40-4)10-7-23)8-12-27(26)43-30(20)17-35(3)16-22-5-11-28-29(13-22)42-19-41-28/h5-14,20-21,30,37H,15-19H2,1-4H3,(H2,33,34,39)/t20-,21-,30-/m0/s1
Release date: 2019-05-15
Human butyrylcholinesterase in complex with (Z)-N-tert-butyl-1-(8-(3-(4-(prop-2-yn-1-yl)piperazin-1-yl)propoxy)quinolin-2-yl)methanimine oxide (PDB entry 7QBR)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 529 residues
Sequence: EDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.1801
R free: 0.2138
Average B factor: 60.78
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate
Matthews coefficient: 3.29
Solvent content (%): 62.63
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: 2022-11-30
Crystal Structure Analysis of PIN1 (PDB entry 6DUN)
Macromolecule: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 122 residues
Sequence: GSHMKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEQITRTQEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.1521
R free: 0.1987
Average B factor: 24.7461
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 2 M ammonium citrate, pH 6.5
Matthews coefficient: 1.98
Solvent content (%): 37.8
Ligand: TRIHYDROXYARSENITE(III) (TAS)
Ligand formula: As H3 O3
Ligand molecular weight: 125.944
Ligand SMILES: O[As](O)O
Ligand InChI: InChI=1S/AsH3O3/c2-1(3)4/h2-4H
Release date: 2019-03-06
Crystal structure of ULK1 in complexed with PF-03814735 (PDB entry 6QAS)
Macromolecule: Serine/threonine-protein kinase ULK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 287 residues
Sequence: GGGSMEPGRGGTETVGKFEFSRKDLIGHGAFAVVFKGRHRAAHDLEVAVKCINKKNLAKSQTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAATLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKTLVPTIPRETSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDASPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.17013
R free: 0.19651
Average B factor: 31.23
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293.15
Crystal growth procedure: 2.8 M Ammonium sulfate, 0.1 M citrate, pH 5.6
Matthews coefficient: 2.36
Solvent content (%): 47.96
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: 2019-02-27
Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole from cocktail screen) (PDB entry 5F6X)
Macromolecule: SUMO-conjugating enzyme UBC9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 157 residues
Sequence: SGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGAAGTPWAGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.17428
R free: 0.19314
Average B factor: 11.124
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 294
Crystal growth procedure: 0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000
Matthews coefficient: 2.73
Solvent content (%): 55.03
Ligand: 5-chloranyl-3~{H}-1,3-benzoxazole-2-thione (5VM)
Ligand formula: C7 H4 Cl N O S
Ligand molecular weight: 185.631
Ligand SMILES: c1cc2c(cc1Cl)NC(=S)O2
Ligand InChI: InChI=1S/C7H4ClNOS/c8-4-1-2-6-5(3-4)9-7(11)10-6/h1-3H,(H,9,11)
Release date: 2016-04-27
Carbonic Anhydrase II Inhibitor RA13 (PDB entry 5NYA)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.117
R free: 0.1377
Average B factor: 14.578
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Tris                                               
1.6 M Natrium Citrate
Matthews coefficient: 2.1
Solvent content (%): 41.5
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: 2018-01-17
Enzyme-substrate complex of TDG catalytic domain bound to a G/U analog (PDB entry 5JXY)
Macromolecule: G/T mismatch-specific thymine DNA glycosylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2.29
Sequence length: 204 residues
Sequence: GSHMASFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNMDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.1979
R free: 0.231
Average B factor: 35.1
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystal growth procedure: 0.2M Ammonium Chloride and 20% PEG3350
Matthews coefficient: 2.4
Solvent content (%): 48.82
Release date: 2016-09-28
Atrial Natriuretic Peptide Receptor complexed with human Atrial Natriuretic Peptide (PDB entry 7BRH)
Macromolecule: Atrial natriuretic peptide receptor 1
Type: Protein, polypeptide(L)
Source organism: Rattus norvegicus
EC number: 4.6.1.2
Sequence length: 435 residues
Sequence: SDLTVAVVLPLTNTSYPWSWARVGPAVELALARVKARPDLLPGWTVRMVLGSSENAAGVCSDTAAPLAAVDLKWEHSPAVFLGPGCVYSAAPVGRFTAHWRVPLLTAGAPALGIGVKDEYALTTRTGPSHVKLGDFVTALHRRLGWEHQALVLYADRLGDDRPCFFIVEGLYMRVRERLNITVNHQEFVEGDPDHYPKLLRAVRRKGRVIYICSSPDAFRNLMLLALNAGLTGEDYVFFHLDVFGQSLKSAQGLVPQKPWERGDGQDRSARQAFQAAKIITYKEPDNPEYLEFLKQLKLLADKKFNFTVEDGLKNIIPASFHDGLLLYVQAVTETLAQGGTVTDGENITQRMWNRSFQGVTGYLKIDRNGDRDTDFSLWDMDPETGAFRVVLNYNGTSQELMAVSEHKLYWPLGYPPPDVPKCGFDNEDPACNQD
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.195
R free: 0.2375
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 300
Crystal growth procedure: Sodium malonate, MES
Matthews coefficient: 3.8
Solvent content (%): 67.59
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: 2021-03-31
Human Argonaute2 Bound to t1-G Target RNA (PDB entry 4Z4D)
Macromolecule: Protein argonaute-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.26
Sequence length: 859 residues
Sequence: MYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQALAKAVQVHQDTLRTMYFA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1631
R free: 0.189
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, Tris, Isopropanol, Phenol, Magnesium
Matthews coefficient: 2.12
Solvent content (%): 41.93
Ligand: PHENOL (IPH)
Ligand formula: C6 H6 O
Ligand molecular weight: 94.111
Ligand SMILES: c1ccc(cc1)O
Ligand InChI: InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H
Release date: 2015-09-23
Factor VIIa in complex with the inhibitor 1-[(2R,15R)-2-[(1-amino-4-fluoroisoquinolin-6-yl)amino]-4,15,17-trimethyl-3,12-dioxo-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaen-7-yl]cyclohexane-1-carboxylic acid (PDB entry 5L2Z)
Macromolecule: Coagulation factor VII (Light Chain)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 58 residues
Sequence: DQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEKR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.181
R free: 0.203
Average B factor: 26.8
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES, pH 6.0, 20 mM CACL2, 17.5%(W/V) PEG 6000
Matthews coefficient: 3.44
Solvent content (%): 64.27
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: 2016-09-28
Crystal structure of IRAK4 in complex with compound 23 (PDB entry 6O8U)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 305 residues
Sequence: SVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTASGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.231
R free: 0.255
Average B factor: 41.754
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 292
Crystal growth procedure: 2.3M-2.7M ammonium sulfate, 0.1M HEPES Na pH 7.0-7.3
Matthews coefficient: 2.65
Solvent content (%): 53.53
Ligand: N-[2,2-dimethyl-6-(morpholin-4-yl)-2,3-dihydro-1-benzofuran-5-yl]pyrazolo[1,5-a]pyrimidine-3-carboxamide (LS7)
Ligand formula: C21 H23 N5 O3
Ligand molecular weight: 393.439
Ligand SMILES: CC1(Cc2cc(c(cc2O1)N3CCOCC3)NC(=O)c4cnn5c4nccc5)C
Ligand InChI: InChI=1S/C21H23N5O3/c1-21(2)12-14-10-16(17(11-18(14)29-21)25-6-8-28-9-7-25)24-20(27)15-13-23-26-5-3-4-22-19(15)26/h3-5,10-11,13H,6-9,12H2,1-2H3,(H,24,27)
Release date: 2019-05-22
Crystal Structure of KDM4A with compound YP-02-145 (PDB entry 6G5X)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 359 residues
Sequence: MASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.1701
R free: 0.2033
Average B factor: 39.5807
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 100mM Citrate, 10mM NiCl2, 20% PEG 3350
Matthews coefficient: 2.51
Solvent content (%): 50.98
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: 2019-04-10
SOD1 and Nanobody2 complex (PDB entry 8K3A)
Macromolecule: Superoxide dismutase [Cu-Zn]
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.15.1.1
Sequence length: 153 residues
Sequence: ATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.74
R work: 0.2341
R free: 0.2555
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Magnesium chloride, 0.1 M Sodium, citrate pH 5, 15%(w/v) PEG 4000
Matthews coefficient: 4.14
Solvent content (%): 70.29
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: 2024-07-17
Human Fyn-SH2 domain in complex with a synthetic high-affinity phospho-peptide (PDB entry 4U1P)
Macromolecule: Tyrosine-protein kinase Fyn
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 122 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMEWYFGKLGRKDAERQLLSFGNPRGTFLIRESETTKGAYSLSIRDWDDMKGDHVKHYKIRKLDNGGYYITTRAQFETLQQLVQHYSERAAGLCCRLVVPCHK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1511
R free: 0.1875
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MOPS/Na HEPES pH 7.5, 0.12 M monosaccharide mixture, PEG 1000, 12.5%(w/v) PEG 3350 and 12.5%(v/v) MPD
Matthews coefficient: 1.79
Solvent content (%): 31.39
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2015-07-29
Crystal structure of Aldo-keto reductase 1C3 complexed with compound 28 (PDB entry 7WQR)
Macromolecule: Aldo-keto reductase family 1 member C3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 329 residues
Sequence: MHHHHHHDSKHQCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKKAQLDYVDLYLIHSPMSLKPGEELSPTDENGKVIFDIVDLCTTWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHYFNSDSFASHPNYPYSDEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.124
R work: 0.2214
R free: 0.2728
Average B factor: 41.4795
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: MES pH 6.0, Ammonium chloride, PEG 6000
Matthews coefficient: 2.06
Solvent content (%): 40.41
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2023-01-04