satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of the human M1 muscarinic acetylcholine receptor bound to antagonist Tiotropium (PDB entry 5CXV)
Macromolecule: Muscarinic acetylcholine receptor M1,Endolysin,Muscarinic acetylcholine receptor M1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 515 residues
Sequence: MKTIIALSYIFCLVFADYKDDDDAAAQTSAPPAVSPQITVLAPGKGPWQVAFIGITTGLLSLATVTGNLLVLISFKVNTELKTVNNYFLLSLACADLIIGTFSMNLYTTYLLMGHWALGTLACDLWLALDYVASQASVMNLLLISFDRYFSVTRPLSYRAKRTPRRAALMIGLAWLVSFVLWAPAILFWQYLVGERTVLAGQCYIQFLSQPIITFGTAMAAFYLPVTVMCTLYWRIYRETENRNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYFSLVKEKKAARTLSAILLAFILTWTPYNIMVLVSTFCKDCVPETLWELGYWLCYVNSTINPMCYALCNKAFRDTFRLLLLCRWDKRRWRKIPKRPGSVHRTPSRQCHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.23133
R free: 0.28204
Average B factor: 73.383
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293
Crystal growth procedure: 33% PEG 300, 100 mM sodium acetate, and 100 mM Bis-Tris Propane (pH 8.0)
Matthews coefficient: 3.09
Solvent content (%): 60.21
Ligand: (1R,2R,4S,5S,7S)-7-{[hydroxy(dithiophen-2-yl)acetyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane (0HK)
Ligand formula: C19 H22 N O4 S2
Ligand molecular weight: 392.512
Ligand SMILES: C[N+]1(C2CC(CC1C3C2O3)OC(=O)C(c4cccs4)(c5cccs5)O)C
Ligand InChI: InChI=1S/C19H22NO4S2/c1-20(2)12-9-11(10-13(20)17-16(12)24-17)23-18(21)19(22,14-5-3-7-25-14)15-6-4-8-26-15/h3-8,11-13,16-17,22H,9-10H2,1-2H3/q+1/t11-,12-,13+,16-,17+
Release date: 2016-03-09
Crystal structure of Dot1L in complex with an inhibitor (compound 3). (PDB entry 6TE6)
Macromolecule: Histone-lysine N-methyltransferase, H3 lysine-79 specific
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 334 residues
Sequence: GPGEKLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKNPG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.178
R free: 0.201
Average B factor: 51.79
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 1.28 M Na/K-tartrate
0.1 M Hepes pH 6.6
Matthews coefficient: 3.5
Solvent content (%): 64.87
Ligand: ~{N}1-[(~{S})-(3-chlorophenyl)-pyridin-2-yl-methyl]-4-methylsulfonyl-~{N}2-pyrimidin-2-yl-benzene-1,2-diamine (N4W)
Ligand formula: C23 H20 Cl N5 O2 S
Ligand molecular weight: 465.955
Ligand SMILES: CS(=O)(=O)c1ccc(c(c1)Nc2ncccn2)NC(c3cccc(c3)Cl)c4ccccn4
Ligand InChI: InChI=1S/C23H20ClN5O2S/c1-32(30,31)18-9-10-19(21(15-18)29-23-26-12-5-13-27-23)28-22(20-8-2-3-11-25-20)16-6-4-7-17(24)14-16/h2-15,22,28H,1H3,(H,26,27,29)/t22-/m0/s1
Release date: 2019-12-11
Crystal structure of human butyrylcholinesterase in complex with N-((1-benzylpiperidin-3-yl)methyl)-N-(2-methoxyethyl)naphthalene-2-sulfonamide (PDB entry 5DYW)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 530 residues
Sequence: TEDDIIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNPNETQNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1899
R free: 0.2165
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M ammonium acetate, 12% polyethylene glycol 4000.
Matthews coefficient: 2.7
Solvent content (%): 54.44
Ligand: N-{[(3S)-1-benzylpiperidin-3-yl]methyl}-N-(2-methoxyethyl)naphthalene-2-sulfonamide (5HF)
Ligand formula: C26 H32 N2 O3 S
Ligand molecular weight: 452.609
Ligand SMILES: COCCN(CC1CCCN(C1)Cc2ccccc2)S(=O)(=O)c3ccc4ccccc4c3
Ligand InChI: InChI=1S/C26H32N2O3S/c1-31-17-16-28(32(29,30)26-14-13-24-11-5-6-12-25(24)18-26)21-23-10-7-15-27(20-23)19-22-8-3-2-4-9-22/h2-6,8-9,11-14,18,23H,7,10,15-17,19-21H2,1H3/t23-/m0/s1
Release date: 2017-01-18
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMSOA000683b (PDB entry 5QFT)
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): 1.96
R work: 0.1897
R free: 0.2372
Average B factor: 45.5118
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: 3.38
Solvent content (%): 63.61
Ligand: 4-[(1H-pyrazol-1-yl)methyl]benzonitrile (JOY)
Ligand formula: C11 H9 N3
Ligand molecular weight: 183.209
Ligand SMILES: c1cnn(c1)Cc2ccc(cc2)C#N
Ligand InChI: InChI=1S/C11H9N3/c12-8-10-2-4-11(5-3-10)9-14-7-1-6-13-14/h1-7H,9H2
Release date: 2018-10-10
TRIM7 in complex with C-terminal peptide of NSP5 (PDB entry 7X6Y)
Macromolecule: E3 ubiquitin-protein ligase TRIM7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 174 residues
Sequence: KEEKVELTLDPDTANPRLILSLDLKGVRLGERAQDLPNHPCRFDTNTRVLASCGFSSGRHHWEVEVGSKDGWAFGVARESVRRKGLTPFTPEEGVWALQLNGGQYWAVTSPERSPLSCGHLSRVRVALDLEVGAVSFYAVEDMRHLYTFRVNFQERVFPLFSVCSTGTYLRIWP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.39
R work: 0.1426
R free: 0.1654
Average B factor: 19.17
Crystallization method: LIQUID DIFFUSION
Crystallization temperature (K): 291.15
Crystal growth procedure: Potassium sodium tartrate tetrahydrate, Tris
Matthews coefficient: 2.4
Solvent content (%): 48.64
Release date: 2022-08-10
Crystal structure of human LTA4H mutant D375N in open conformation (crystal form II) (PDB entry 5NID)
Macromolecule: Leukotriene A-4 hydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 617 residues
Sequence: MHHHHHHPEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPNVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.568
R work: 0.1821
R free: 0.2098
Average B factor: 50.64
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 8% (w/v) PEG 20 000, 15% (w/v) PEG MME 550, 100 mM Hepes/MOPS pH 7.7-8.0, 15 mM CaCl2, 15 mM MgCl2
Matthews coefficient: 2.56
Solvent content (%): 52
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2017-08-23
Crystal structure of the epidermal growth factor receptor extracellular region with R84K mutation in complex with epiregulin crystallized with trehalose (PDB entry 7LEN)
Macromolecule: Isoform 4 of Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 507 residues
Sequence: LEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIKGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2368
R free: 0.2946
Average B factor: 86.6232
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 8 mg/ml protein, 100 mM HEPES (pH 7.5), 12% PEG3350, with 3% (w/v) D-(+)-trehalose dihydrate
Matthews coefficient: 2.64
Solvent content (%): 53
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: 2021-11-17
Crystal structure of JAK2 JH2-V617F in complex with Cdk2 inhibitor IV (PDB entry 8B8N)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCFCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.2092
R free: 0.2548
Average B factor: 60.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Tris pH 8, 20% PEG4000, 0.2M Na-acetate
Matthews coefficient: 2.4
Solvent content (%): 48.71
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: 2023-02-01
Crystal structure of SHP2 in complex with JAB-3186 (PDB entry 8WX7)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 526 residues
Sequence: GMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.19463
R free: 0.24599
Average B factor: 41.431
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M HEPES pH 7.5, 0.2 M ammonium sulphate, 28 % w/v PEG3350
Matthews coefficient: 2.22
Solvent content (%): 44.65
Ligand: (5~{S})-1'-[6-azanyl-5-(2-azanyl-3-chloranyl-pyridin-4-yl)sulfanyl-pyrazin-2-yl]spiro[5,7-dihydrocyclopenta[b]pyridine-6,4'-piperidine]-5-amine (XD8)
Ligand formula: C21 H23 Cl N8 S
Ligand molecular weight: 454.979
Ligand SMILES: c1cc2c(nc1)CC3(C2N)CCN(CC3)c4cnc(c(n4)N)Sc5ccnc(c5Cl)N
Ligand InChI: InChI=1S/C21H23ClN8S/c22-16-14(3-7-27-18(16)24)31-20-19(25)29-15(11-28-20)30-8-4-21(5-9-30)10-13-12(17(21)23)2-1-6-26-13/h1-3,6-7,11,17H,4-5,8-10,23H2,(H2,24,27)(H2,25,29)/t17-/m1/s1
Release date: 2024-08-14
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOOA000595a (PDB entry 5QG9)
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): 1.671
R work: 0.1976
R free: 0.2266
Average B factor: 40.2983
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 (%): 63.12
Ligand: (1S,3S,4R)-3-[(1S)-1-hydroxypropyl]-2-(methylsulfonyl)-2-azabicyclo[2.2.2]octan-4-ol (JQ4)
Ligand formula: C11 H21 N O4 S
Ligand molecular weight: 263.354
Ligand SMILES: CCC(C1C2(CCC(N1S(=O)(=O)C)CC2)O)O
Ligand InChI: InChI=1S/C11H21NO4S/c1-3-9(13)10-11(14)6-4-8(5-7-11)12(10)17(2,15)16/h8-10,13-14H,3-7H2,1-2H3/t8-,9-,10-,11-/m0/s1
Release date: 2018-10-10
Crystal structure of CDK2 liganded with compound EF4195 (PDB entry 7SA0)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.1947
R free: 0.2186
Average B factor: 37.0855
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 4.5mg/mL CDK2 crystalized in 50mM Na/KPO4, pH6.9, 50mM Hepes Na, pH7.5, 5% v/v PEG3350 were soaked overnight with 2.5mM EF4195 in 50mM Hepes Na, pH7.5, 10% v/v PEG3350
Matthews coefficient: 2.08
Solvent content (%): 40.88
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: 2022-10-05
Crystal structure of human carbonic anhydrase I in complex with the inhibitor famotidine (PDB entry 6G3V)
Macromolecule: Carbonic anhydrase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 261 residues
Sequence: MASPDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.2142
R free: 0.2631
Average B factor: 30.799
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 9
Crystallization temperature (K): 296
Crystal growth procedure: 28% PEG4000, 0.2 M sodium acetate, Tris 100 mM
Matthews coefficient: 2.34
Solvent content (%): 47.5
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: 2018-11-28
Crystal structure of the human DEAH-helicase DHX15 in complex with the NKRF G-patch (PDB entry 6SH7)
Macromolecule: Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 689 residues
Sequence: GPHMLEQCINPFTNLPHTPRYYDILKKRLQLPVWEYKDRFTDILVRHQSFVLVGETGSGKTTQIPQWCVEYMRSLPGPKRGVACTQPRRVAAMSVAQRVADEMDVMLGQEVGYSIRFEDCSSAKTILKYMTDGMLLREAMNDPLLERYGVIILDEAHERTLATDILMGVLKEVVRQRSDLKVIVMSATLDAGKFQIYFDNCPLLTIPGRTHPVEIFYTPEPERDYLEAAIRTVIQIHMCEEEEGDLLLFLTGQEEIDEACKRIKREVDDLGPEVGDIKIIPLYSTLPPQQQQRIFEPPPPKKQNGAIGRKVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVTAISKASAQQRAGRAGRTRPGKCFRLYTEKAYKTEMQDNTYPEILRSNLGSVVLQLKKLGIDDLVHFDFMDPPAPETLMRALELLNYLAALNDDGDLTELGSMMAEFPLDPQLAKMVIASCDYNCSNEVLSITAMLSVPQCFVRPTEAKKAADEAKMRFAHIDGDHLTLLNVYHAFKQNHESVQWCYDNFINYRSLMSADNVRQQLSRIMDRFNLPRRSTDFTSRDYYINIRKALVTGYFMQVAHLERTGHYLTVKDNQVVQLHPSTVLDHKPEWVLYNEFVLTTKNYIRTCTDIKPEWLVKIAPQYYDMSNFPQCEAKRQLDRIIAKLQSKEYSQY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.209
R free: 0.2508
Average B factor: 79.88
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1 M carboxylic acids, 0.1 M BICINE/Tris pH 8.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD
Matthews coefficient: 2.43
Solvent content (%): 49.37
Release date: 2020-04-22
Room temperature structure of the human Serine/Threonine Kinase 17B (STK17B/DRAK2) in complex with ADP at atmospheric pressure (PDB entry 7Q7C)
Macromolecule: Serine/threonine-protein kinase 17B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 327 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMENFNNFYILTSKELGRGKFAVVRQCISKSTGQEYAAKFLKKRRRGQDCRAEILHEIAVLELAKSCPRVINLHEVYENTSEIILILEYAAGGEIFSLCLPELAEMVSENDVIRLIKQILEGVYYLHQNNIVHLDLKPQNILLSSIYPLGDIKIVDFGMSRKIGHACELREIMGTPEYLAPEILNYDPITTATDMWNIGIIAYMLLTHTSPFVGEDNQETYLNISQVNVDYSEETFSSVSQLATDFIQSLLVKNPEKRPTAEICLSHSWLQQWDFENLFHPEETSSSSQTQDHSVRSSEDKTSKSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2072
R free: 0.2376
Average B factor: 97.15
Crystallization method: BATCH MODE
Crystallization temperature (K): 295
Crystal growth procedure: 20 mg/ml protein in 25 mM HEPES pH 7.5, 500 mM NaCl, 0.5 mM TCEP was mixed 1:1.5 with precipitant solution (0.1 M HEPES 6.5, 0.2M ammonium acetate, 20% PEG 3350, 50mM sodium/potassium tartrate, 0.8mM quercetin). Batch grown crystals were subsequently mixed 1:1 with 100 mM ATP/50mM magnesium chloride in DRAK2 crystallization buffer and incubated for half an hour.
Matthews coefficient: 2.78
Solvent content (%): 55.82
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: 2022-11-16
Truncated mitofusin-1, GDP-bound (PDB entry 5GOE)
Macromolecule: Mitofusin-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 422 residues
Sequence: GPHMGGSMAEPVSPLKHFVLAKKAITAIFDQLLEFVTEGSHFVEATYKNPELDRIATEDDLVEMQGYKDKLSIIGEVLSRRHMKVAFFGRTSSGKSSVINAMLWDKVLPSGIGHITNCFLSVEGTDGDKAYLMTEGSDEKKSVKTVNQLAHALHMDKDLKAGCLVRVFWPKAKCALLRDDLVLVDSPGTDVTTELDSWIDKFCLDADVFVLVANSESTLMNTEKHFFHKVNERLSKPNIFILNNRWDASASEPEYMEDVRRQHMERCLHFLVEELKVVNALEAQNRIFFVSAKEVLSARKQKAQGMPESGVALAEGFHARLQEFQNFEQIFEECISQSAVKTKFEQHTIRAKQILATVKNIMDSVNLAAEDKRHYSARLPKEIDQLEKIQNNSKLLRNKAVQLENELENFTKQFLPSSNEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.801
R work: 0.177
R free: 0.2042
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M ammonium citrate tribasic and 20% PEG 3350
Matthews coefficient: 2.55
Solvent content (%): 51.75
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2017-01-25
Carbonic Anhydrase CAIX mimic in complex with inhibitor JS13 (PDB entry 6GXB)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.11277
R free: 0.15376
Average B factor: 13.18
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: protein 25 mg/mL, 1.6M sodium citrate, 50mM Tris H2SO4 pH 7.8
Matthews coefficient: 2.09
Solvent content (%): 41.04
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: 2019-05-08
Crystal structure of DYRK2 in complex with EHT 5372 (Compound 1) (PDB entry 5LXC)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 408 residues
Sequence: SMGKVKATPMTPEQAMKQYMQKLTAFEHHEIFSYPEIYFLGLNAKKRQGMTGGPNNGGYDDDQGSYVQVPHDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTYIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRRLPKPPTGEKTSVKR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.20564
R free: 0.25401
Average B factor: 49.867
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 25% PEG 3350, 0.2 M NaCl and 0.1 M bis-tris, pH 5.5
Matthews coefficient: 3.04
Solvent content (%): 59.5
Ligand: methyl 9-[(2,4-dichlorophenyl)amino]-[1,3]thiazolo[5,4-f]quinazoline-2-carboximidate (7AA)
Ligand formula: C17 H11 Cl2 N5 O S
Ligand molecular weight: 404.273
Ligand SMILES: COC(=N)c1nc2ccc3c(c2s1)c(ncn3)Nc4ccc(cc4Cl)Cl
Ligand InChI: InChI=1S/C17H11Cl2N5OS/c1-25-15(20)17-24-12-5-4-11-13(14(12)26-17)16(22-7-21-11)23-10-3-2-8(18)6-9(10)19/h2-7,20H,1H3,(H,21,22,23)/b20-15+
Release date: 2016-10-26