satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of JmjC domain of human histone demethylase UTY in complex with D-2-hydroxyglutarate (PDB entry 5FYM)
Macromolecule: HISTONE DEMETHYLASE UTY
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 478 residues
Sequence: MLPKDKLNPPTPSIYLENKRDAFFPPLHQFCTNPKNPVTVIRGLAGALKLDLGLFSTKTLVEANNEHMVEVRTQLLQPADENWDPTGTKKIWRCESNRSHTTIAKYAQYQASSFQESLREENEKRTQHKDHSDNESTSSENSGRRRKGPFKTIKFGTNIDLSDNKKWKLQLHELTKLPAFARVVSAGNLLTHVGHTILGMNTVQLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFVVPEDYWGVLNDFCEKNNLNFLMSSWWPNLEDLYEANVPVYRFIQRPGDLVWINAGTVHWVQAVGWCNNIAWNVGPLTACQYKLAVERYEWNKLKSVKSPVPMVHLSWNMARNIKVSDPKLFEMIKYCLLKILKQYQTLREALVAAGKEVIWHGRTNDEPAHYCSICEVEVFNLLFVTNESNTQKTYIVHCHDCARKTSKSLENFVVLEQYKMEDLIQVYDQFTLALSLSSSSAENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1922
R free: 0.245
Crystallization pH: 7.4
Crystal growth procedure: 0.1M HEPES PH 7.4, 0.2M TRIMETHYLAMINE N-OXIDE, 15% PEG3350
Matthews coefficient: 2.84
Solvent content (%): 56.76
Ligand: (2R)-2-hydroxypentanedioic acid (2HG)
Ligand formula: C5 H8 O5
Ligand molecular weight: 148.114
Ligand SMILES: C(CC(=O)O)C(C(=O)O)O
Ligand InChI: InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m1/s1
Release date: 2016-03-16
Crystal Structure of human Legumain in complex with (2S)-N-[(3S)-5-amino-1-(1,3-oxazol-2-yl)-5-oxopent-1-yn-3-yl]-1-[1-[4-(trifluoromethoxy)phenyl]cyclopropanecarbonyl]pyrrolidine-2-carboxamide (PDB entry 7FQK)
Macromolecule: Legumain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.34
Sequence length: 444 residues
Sequence: MKLCILLAVVAFVGLSLGVPIDDPEDGGKHWVVIVAGSNGWYNYRHQADACHAYQIIHRNGIPDEQIVVMMYDDIAYSEDNPTPGIVINRPNGTDVYQGVPKDYTGEDVTPQNFLAVLRGDAEAVKGIGSGKVLKSGPQDHVFIYFTNHGSTGILVFPNEDLHVKDLNETIHYMYKHKMYRKMVFYIEACESGSMMNHLPDNINVYATTAANPRESSYACYYDEKRSTYLGDWYSVNWMEDSDVEDLTKETLHKQYHLVKSHTNTSHVMQYGQKTISTMKVMQFQGMKRKASSPVPLPPVTHLDLTPSPDVPLTIMKRKLMNTNDLEESRQLTEEIQRHLDARHLIEKSVRKIVSLLAASEAEVEQLLSERAPLTGHSCYPEALLHFRTHCFNWHSPTYEYALRHLYVLVNLCEKPYPLHRIKLSMDHVCLGHYVDHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.194
R free: 0.2325
Average B factor: 40.431
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 28.5mg/mL protein in 25mM HEPES/NaOH pH7, 300 mM NaCl, 200mM Trehalose incubated with 10-fold excess of ligand, then mixed 50-70% with 50-30% reservoir consisting of 20% v/v PEG smear broad, 0.1M MES/NaOH pH 6.5, total volume 200nL
Matthews coefficient: 2.21
Solvent content (%): 44.39
Ligand: N-[(1E,3R)-5-amino-1-(1,3-oxazol-2-yl)-5-oxopent-1-en-3-yl]-1-{1-[4-(trifluoromethoxy)phenyl]cyclopropane-1-carbonyl}-L-prolinamide (WS9)
Ligand formula: C24 H25 F3 N4 O5
Ligand molecular weight: 506.474
Ligand SMILES: c1cc(ccc1C2(CC2)C(=O)N3CCCC3C(=O)NC(CC(=O)N)C=Cc4ncco4)OC(F)(F)F
Ligand InChI: InChI=1S/C24H25F3N4O5/c25-24(26,27)36-17-6-3-15(4-7-17)23(9-10-23)22(34)31-12-1-2-18(31)21(33)30-16(14-19(28)32)5-8-20-29-11-13-35-20/h3-8,11,13,16,18H,1-2,9-10,12,14H2,(H2,28,32)(H,30,33)
Release date: 2023-10-11
Human PFKFB3 in complex with a N-Aryl 6-Aminoquinoxaline inhibitor 4 (PDB entry 6IC0)
Macromolecule: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.105
Sequence length: 428 residues
Sequence: ELTQSRVQKIWVPVNSPTVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNVGEYRREAVKQYSSYNFFRPDNEEAMKVRKQCALAALRDVKSYLAKEGGQIAVFDATNTTRERRHMILHFAKENDFKAFFIESVCDDPTVVASNIMEVKISSPDYKDCNSAEAMDDFMKRISCYEASYQPLDPDKCDRDLSLIKVIDVGRRFLVNRVQDHIQSRIVYYLMNIHVQPRTIYLCRHGENEHNLQGRIGGDSGLSSRGKKFASALSKFVEEQNLKDLRVWTSQLKSTIQTAEALRLPYEQWKALNEIDAGVCEELTYEEIRDTYPEEYALREQDKYYYRYPTGESYQDLVQRLEPVIMELERQENVLVICHQAVLRCLLAYFLDKSAEEMPYLKCPLHTVLKLTPVAYGCRVESIYLNVESVCTHRERS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1907
R free: 0.2547
Average B factor: 47.159
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2% Tacsimate, pH7.0; 5% 2-propanol; 0.1M imidazole; 8% PEG3350
Matthews coefficient: 3.79
Solvent content (%): 67.57
Ligand: 3-[[8-(1-methylindol-6-yl)quinoxalin-6-yl]amino]-~{N}-pyrimidin-5-yl-pyridine-4-carboxamide (HAK)
Ligand formula: C27 H20 N8 O
Ligand molecular weight: 472.501
Ligand SMILES: Cn1ccc2c1cc(cc2)c3cc(cc4c3nccn4)Nc5cnccc5C(=O)Nc6cncnc6
Ligand InChI: InChI=1S/C27H20N8O/c1-35-9-5-17-2-3-18(10-25(17)35)22-11-19(12-23-26(22)32-8-7-31-23)33-24-15-28-6-4-21(24)27(36)34-20-13-29-16-30-14-20/h2-16,33H,1H3,(H,34,36)
Release date: 2019-01-23
Crystal Structure of human phosphodiesterase 10 in complex with N-[(3R)-1-(5-chloropyridin-2-yl)pyrrolidin-3-yl]-1-methyl-4-pyridin-4-ylpyrazole-3-carboxamide (PDB entry 5SK0)
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): 2.02
R work: 0.1618
R free: 0.1868
Average B factor: 39.415
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: 2.7
Solvent content (%): 54.37
Ligand: N-[(3R)-1-(5-chloropyridin-2-yl)pyrrolidin-3-yl]-1-methyl-4-(pyridin-4-yl)-1H-pyrazole-3-carboxamide (KAU)
Ligand formula: C19 H19 Cl N6 O
Ligand molecular weight: 382.847
Ligand SMILES: Cn1cc(c(n1)C(=O)NC2CCN(C2)c3ccc(cn3)Cl)c4ccncc4
Ligand InChI: InChI=1S/C19H19ClN6O/c1-25-12-16(13-4-7-21-8-5-13)18(24-25)19(27)23-15-6-9-26(11-15)17-3-2-14(20)10-22-17/h2-5,7-8,10,12,15H,6,9,11H2,1H3,(H,23,27)/t15-/m1/s1
Release date: 2022-10-12
CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 4-(6-(cyclohexylamino)-8-(((tetrahydro-2H-pyran-4-yl)methyl)amino)imidazo[1,2-b]pyridazin-3-yl)-N-cyclopropylbenzamide (PDB entry 3WZJ)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 321 residues
Sequence: MECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTTEEMKYVLGQLVGLNLVPRGSAAGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2205
R free: 0.282
Average B factor: 63.813
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris hydrochloride pH7.5, 0.12M magnesium chloride, 8%(w/v) triethylene glycol 
, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Matthews coefficient: 3.04
Solvent content (%): 59.51
Ligand: 4-{6-(cyclohexylamino)-8-[(tetrahydro-2H-pyran-4-ylmethyl)amino]imidazo[1,2-b]pyridazin-3-yl}-N-cyclopropylbenzamide (O43)
Ligand formula: C28 H36 N6 O2
Ligand molecular weight: 488.624
Ligand SMILES: c1cc(ccc1c2cnc3n2nc(cc3NCC4CCOCC4)NC5CCCCC5)C(=O)NC6CC6
Ligand InChI: InChI=1S/C28H36N6O2/c35-28(32-23-10-11-23)21-8-6-20(7-9-21)25-18-30-27-24(29-17-19-12-14-36-15-13-19)16-26(33-34(25)27)31-22-4-2-1-3-5-22/h6-9,16,18-19,22-23,29H,1-5,10-15,17H2,(H,31,33)(H,32,35)
Release date: 2015-02-11
Structure of human PRC2-EZH1 containing phosphorylated SUZ12 (PDB entry 7TD5)
Macromolecule: Histone-lysine N-methyltransferase EZH1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.356
Sequence length: 747 residues
Sequence: MEIPNPPTSKCITYWKRKVKSEYMRLRQLKRLQANMGAKALYVANFAKVQEKTQILNEEWKKLRVQPVQSMKPVSGHPFLKKCTIESIFPGFASQHMLMRSLNTVALVPIMYSWSPLQQNFMVEDETVLCNIPYMGDEVKEEDETFIEELINNYDGKVHGEEEMIPGSVLISDAVFLELVDALNQYSDEEEEGHNDTSDGKQDDSKEDLPVTRKRKRHAIEGNKKSSKKQFPNDMIFSAIASMFPENGVPDDMKERYRELTEMSDPNALPPQCTPNIDGPNAKSVQREQSLHSFHTLFCRRCFKYDCFLHPFHATPNVYKRKNKEIKIEPEPCGTDCFLLLEGAKEYAMLHNPRSKCSGRRRRRHHIVSASCSNASASAVAETKEGDSDRDTGNDWASSSSEANSRCQTPTKQKASPAPPQLCVVEAPSEPVEWTGAEESLFRVFHGTYFNNFCSIARLLGTKTCKQVFQFAVKESLILKLPTDELMNPSQKKKRKHRLWAAHCRKIQLKKDNSSTQVYNYQPCDHPDRPCDSTCPCIMTQNFCEKFCQCNPDCQNRFPGCRCKTQCNTKQCPCYLAVRECDPDLCLTCGASEHWDCKVVSCKNCSIQRGLKKHLLLAPSDVAGWGTFIKESVQKNEFISEYCGELISQDEADRRGKVYDKYMSSFLFNLNNDFVVDATRKGNKIRFANHSVNPNCYAKVVMVNGDHRIGIFAKRAIQAGEELFFDYRYSQADALKYVGIERETDVL
Oligomeric state: Hetero 5-mer
Stoichiometry: A2, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.994
R work: 0.1957
R free: 0.2299
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 10% PEG3350, 100 mM (NH4)2SO4, 50mM HEPES 6.8
Matthews coefficient: 2.95
Solvent content (%): 58.3
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: 2022-11-16
Crystal structure of the catalytic domain of human PKC alpha (D463N, V568I, S657E) in complex with Darovasertib (NVP-LXS196) at 2.82-A resolution (PDB entry 8UAK)
Macromolecule: Protein kinase C alpha type
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.13
Sequence length: 354 residues
Sequence: GPSEDRKQPSNNLDRVKLTDFNFLMVLGKGSFGKVMLADRKGTEELYAIKILKKDVVIQDDDVECTMVEKRVLALLDKPPFLTQLHSCFQTVDRLYFVMEYVNGGDLMYHIQQVGKFKEPQAVFYAAEISIGLFFLHKRGIIYRNLKLDNVMLDSEGHIKIADFGMCKEHMMDGVTTRTFCGTPDYIAPEIIAYQPYGKSVDWWAYGVLLYEMLAGQPPFDGEDEDELFQSIMEHNVSYPKSLSKEAVSICKGLMTKHPAKRLGCGPEGERDVREHAFFRRIDWEKLENREIQPPFKPKVCGKGAENFDKFFTRGQPVLTPPDQLVIANIDQSDFEGFEYVNPQFVHPILQSAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.82
R work: 0.206
R free: 0.243
Average B factor: 100.13
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 21 mg/mL protein in 50 mM imidazole, 200 mM sodium chloride, 2 mM TCEP, 1 mM NAF, 1% glycerol, pH 8.0 against 0.1 M Bis-Tris, pH 5.5, 18% PEG3350, 0.2 M magnesium chloride
Matthews coefficient: 2.35
Solvent content (%): 47.7
Ligand: (6M)-3-amino-N-[3-(4-amino-4-methylpiperidin-1-yl)pyridin-2-yl]-6-[3-(trifluoromethyl)pyridin-2-yl]pyrazine-2-carboxamide (W39)
Ligand formula: C22 H23 F3 N8 O
Ligand molecular weight: 472.466
Ligand SMILES: CC1(CCN(CC1)c2cccnc2NC(=O)c3c(ncc(n3)c4c(cccn4)C(F)(F)F)N)N
Ligand InChI: InChI=1S/C22H23F3N8O/c1-21(27)6-10-33(11-7-21)15-5-3-9-29-19(15)32-20(34)17-18(26)30-12-14(31-17)16-13(22(23,24)25)4-2-8-28-16/h2-5,8-9,12H,6-7,10-11,27H2,1H3,(H2,26,30)(H,29,32,34)
Release date: 2024-01-24
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z108545814 (PDB entry 7G83)
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): 1.31
R work: 0.1855
R free: 0.2054
Average B factor: 25
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: 2.53
Solvent content (%): 51.31
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2023-07-12
Crystal structure of hEphB1 bound with ADP (PDB entry 7KPM)
Macromolecule: Ephrin type-B receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 279 residues
Sequence: AKEIDVSFVKIEEVIGAGEFGEVYKGRLKLPGKREIYVAIKTLKAGYSEKQRRDFLSEASIMGQFDHPNIIRLEGVVTKSRPVMIITEFMENGALDSFLRQNDGQFTVIQLVGMLRGIAAGMKYLAEMNYVHRDLAARNILVNSNLVCKVSDFGLSRYLQDDTSDPTYTSSLGGKIPVRWTAPEAIAYRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPMDCPAALHQLMLDCWQKDRNSRPRFAEIVNTLDKMIRNPASLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.608
R work: 0.167
R free: 0.1973
Average B factor: 18.8469
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M sodium malonate, pH 4.6, 14% PEG3350
Matthews coefficient: 2.49
Solvent content (%): 50.56
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2021-03-10
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000324a (PDB entry 5QFN)
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): 1.675
R work: 0.1839
R free: 0.2069
Average B factor: 37.1381
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: 3.37
Solvent content (%): 63.45
Ligand: 3-chloro-N-(1-hydroxy-2-methylpropan-2-yl)benzamide (JOV)
Ligand formula: C11 H14 Cl N O2
Ligand molecular weight: 227.687
Ligand SMILES: CC(C)(CO)NC(=O)c1cccc(c1)Cl
Ligand InChI: InChI=1S/C11H14ClNO2/c1-11(2,7-14)13-10(15)8-4-3-5-9(12)6-8/h3-6,14H,7H2,1-2H3,(H,13,15)
Release date: 2018-10-10
Crystal structure of human RPP40 (PDB entry 6AHV)
Macromolecule: Ribonuclease P protein subunit p40
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.26.5
Sequence length: 363 residues
Sequence: MATLRRLREAPRHLLVCEKSNFGNHKSRHRHLVQTHYYNYRVSFLIPECGILSEELKNLVMNTGPYYFVKNLPLHELITPEFISTFIKKGSCYALTYNTHIDEDNTVALLPNGKLILSLDKDTYEETGLQGHPSQFSGRKIMKFIVSIDLMELSLNLDSKKYERISWSFKEKKPLKFDFLLAWHKTGSEESTMMSYFSKYQIQEHQPKVALSTLRDLQCPVLQSSELEGTPEVSCRALELFDWLGAVFSNVDLNNEPNNFISTYCCPEPSTVVAKAYLCTITGFILPEKICLLLEHLCHYFDEPKLAPWVTLSVQGFADSPVSWEKNEHGFRKGGEHLYNFVIFNNQDYWLQMAVGANDHCPP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2179
R free: 0.2531
Average B factor: 49.6534
Crystallization method: EVAPORATION
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 5% v/v TacsimateTM pH 7.0, 100mM Hepes pH 7.0, 10% w/v polyethylene glycol monomethyl ether 5000
Matthews coefficient: 3.32
Solvent content (%): 63
Release date: 2018-12-05
DYRK1A in complex with HG-8-60-1 (PDB entry 6EIJ)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 368 residues
Sequence: GASDSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADEGTNTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.42
R work: 0.21341
R free: 0.24192
Average B factor: 50.255
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M KSCN; 0.05M KCl; 10% PEG 3350, pH 6.8
Matthews coefficient: 2.63
Solvent content (%): 53.24
Ligand: ~{N}-[5-[3-(2-morpholin-4-ylethylcarbamoylamino)phenyl]-[1,3]thiazolo[5,4-b]pyridin-2-yl]cyclopropanecarboxamide (B5Z)
Ligand formula: C23 H26 N6 O3 S
Ligand molecular weight: 466.556
Ligand SMILES: c1cc(cc(c1)NC(=O)NCCN2CCOCC2)c3ccc4c(n3)sc(n4)NC(=O)C5CC5
Ligand InChI: InChI=1S/C23H26N6O3S/c30-20(15-4-5-15)28-23-27-19-7-6-18(26-21(19)33-23)16-2-1-3-17(14-16)25-22(31)24-8-9-29-10-12-32-13-11-29/h1-3,6-7,14-15H,4-5,8-13H2,(H2,24,25,31)(H,27,28,30)
Release date: 2018-08-29
Phospholipase C gamma-1 C-terminal SH2 domain bound to a phosphopeptide derived from the receptor tyrosine kinase ErbB2 (PDB entry 5TQS)
Macromolecule: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
Type: Protein, polypeptide(L)
Source organism: Bos taurus
EC number: 3.1.4.11
Sequence length: 101 residues
Sequence: GSHMHESKEWYHASLTRAQAEHMLMRVPRDGAFLVRKRNEPNSYAISFRAEGKIKHCRVQQEGQTVMLGNSEFDSLVDLISYYEKHPLYRKMKLRYPINEE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.876
R work: 0.1885
R free: 0.237
Average B factor: 36.9937
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M sodium acetate (pH 5.5), 22% PEG MME 5000
Matthews coefficient: 1.95
Solvent content (%): 36.98
Release date: 2017-04-19
Human adenylate kinase 1 (hAK1) mutant-R128W (PDB entry 7DE3)
Macromolecule: Adenylate kinase isoenzyme 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.4.3
Sequence length: 194 residues
Sequence: MEEKLKKTKIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTGDLLRSEVSSGSARGKKLSEIMEKGQLVPLETVLDMLRDAMVAKVNTSKGFLIDGYPREVQQGEEFERRIGQPTLLLYVDAGPETMTQWLLKRGETSGRVDDNEETIKKRLETYYKATEPVIAFYEKRGIVRKVNAEGSVDSVFSQVCTHLDALK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.197
R work: 0.205
R free: 0.2595
Average B factor: 32.0887
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG 3350,0.2M Ammonium acetate
Matthews coefficient: 2.5
Solvent content (%): 50.85
Release date: 2021-11-10
apo-Carbonic Anhydrase II soaked in 3NPA after UV at 160 K (PDB entry 7Y2N)
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): 1.25
R work: 0.11796
R free: 0.16062
Average B factor: 15.591
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.09
Solvent content (%): 41.13
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: 2023-12-20
Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with alpha-D-glucopyranosyl 1,3,4-trisphosphate/ATP/Mn (PDB entry 8PPH)
Macromolecule: Inositol-trisphosphate 3-kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.127
Sequence length: 279 residues
Sequence: GSHMSWVQLAGHTGSFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.19818
R free: 0.23069
Average B factor: 44.291
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.84 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. 
Protein:precipitant ratio 1:1. 
Protein concentration: 18 mg/ml. 
Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. 
Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ATP and 3 mM MnCl2.
Matthews coefficient: 2.67
Solvent content (%): 53.94
Ligand: ADENOSINE-5'-TRIPHOSPHATE (ATP)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2024-02-28
Crystal structure of the human METTL3-METTL14 complex bound to Compound 21 (ADO_AD_089) (PDB entry 7O2E)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2057
R free: 0.273
Average B factor: 62.27
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.15
Solvent content (%): 42.66
Ligand: 4-[4-[(4,4-dimethylpiperidin-1-yl)methyl]-3-fluoranyl-phenyl]-9-[6-(methylamino)pyrimidin-4-yl]-1,4,9-triazaspiro[5.5]undecan-2-one (UZH)
Ligand formula: C27 H38 F N7 O
Ligand molecular weight: 495.635
Ligand SMILES: CC1(CCN(CC1)Cc2ccc(cc2F)N3CC(=O)NC4(C3)CCN(CC4)c5cc(ncn5)NC)C
Ligand InChI: InChI=1S/C27H38FN7O/c1-26(2)6-10-33(11-7-26)16-20-4-5-21(14-22(20)28)35-17-25(36)32-27(18-35)8-12-34(13-9-27)24-15-23(29-3)30-19-31-24/h4-5,14-15,19H,6-13,16-18H2,1-3H3,(H,32,36)(H,29,30,31)
Release date: 2021-09-01