satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of human NTHL1 (PDB entry 7RDS)
Macromolecule: Isoform 3 of Endonuclease III-like protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 257 residues
Sequence: MLRVAYEGSDSEKGEGAEPLKVPVWEPQDWQQQLVNIRAMRNKKDAPVDHLGTEHCYDSSAPPKVRRYQVLLSLMLSSQTKDQVTAGAMQRLRARGLTVDSILQTDDATLGKLIYPVGFWRSKVKYIKQTSAILQQHYGGDIPASVAELVALPGVGPKMAHLAMAVAWGTVSGIAVDTHVHRIANRLRWTKKATKSPEETRAALEEWLPRELWHEINGLLVGFGQQTCLPVHPRCHACLNQALCPAAQGLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1996
R free: 0.2445
Average B factor: 88.64
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: PEG 5K MME, Sodium chloride, Tricine
Matthews coefficient: 3.32
Solvent content (%): 62.96
Ligand: IRON/SULFUR CLUSTER (SF4)
Ligand formula: Fe4 S4
Ligand molecular weight: 351.64
Ligand SMILES: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
Ligand InChI: InChI=1S/4Fe.4S
Release date: 2021-12-29
High-resolution X-ray cocrystal structure of USP7 in complex with LX04-46 (PDB entry 7XHK)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 348 residues
Sequence: SKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFHYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2203
R free: 0.264
Average B factor: 62.1903
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 289
Crystal growth procedure: 20mg/ml Crystal, 100mM Tris,20% PEG 1000, PH 7.0
Matthews coefficient: 2.82
Solvent content (%): 56.45
Ligand: ~{N}-[[4-[6-[[1-[[2-chloranyl-4-(furan-2-yl)phenyl]methyl]-4-oxidanyl-piperidin-4-yl]methyl]-2-methyl-7-oxidanylidene-pyrazolo[4,3-d]pyrimidin-3-yl]phenyl]methyl]methanamide (DVU)
Ligand formula: C31 H31 Cl N6 O4
Ligand molecular weight: 587.069
Ligand SMILES: Cn1c(c2c(n1)C(=O)N(C=N2)CC3(CCN(CC3)Cc4ccc(cc4Cl)c5ccco5)O)c6ccc(cc6)CNC=O
Ligand InChI: InChI=1S/C31H31ClN6O4/c1-36-29(22-6-4-21(5-7-22)16-33-20-39)27-28(35-36)30(40)38(19-34-27)18-31(41)10-12-37(13-11-31)17-24-9-8-23(15-25(24)32)26-3-2-14-42-26/h2-9,14-15,19-20,41H,10-13,16-18H2,1H3,(H,33,39)
Release date: 2023-06-14
HUMAN PI3KDELTA IN COMPLEX WITH LIGAND LASW1976 (PDB entry 6G6W)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 1072 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQGAMGSMPPGVDCPMEFWTKEENQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPEAYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYSFPLQLEPSAQTWGPGTLRLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKATVFRQPLVEQPEDYTLQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNPAPQVQKPRAKPPPIPAKKPSSVSLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKAKKARSTKKKSKKADCPIAWANLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAPHPVYYPALEKILELGRHSECVHVTEEEQLQLREILERRGSGELYEHEKDLVWKLRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLDRALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEALSHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEAGSGGSVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLNKSNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNFKTKFGINRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRESWKTKVNWLAHNVSKDNRQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.72
R work: 0.2181
R free: 0.2601
Average B factor: 96.97
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: PEG
Matthews coefficient: 2.66
Solvent content (%): 53.83
Ligand: ~{N}-[3-[4-[[(1~{S})-1-(5-methyl-4-oxidanylidene-3-phenyl-pyrrolo[2,1-f][1,2,4]triazin-2-yl)ethyl]amino]-7~{H}-pyrrolo[
2,3-d]pyrimidin-5-yl]-5-oxidanyl-phenyl]methanesulfonamide (EO5)
Ligand formula: C28 H26 N8 O4 S
Ligand molecular weight: 570.622
Ligand SMILES: Cc1ccn2c1C(=O)N(C(=N2)C(C)Nc3c4c(c[nH]c4ncn3)c5cc(cc(c5)O)NS(=O)(=O)C)c6ccccc6
Ligand InChI: InChI=1S/C28H26N8O4S/c1-16-9-10-35-24(16)28(38)36(20-7-5-4-6-8-20)27(33-35)17(2)32-26-23-22(14-29-25(23)30-15-31-26)18-11-19(13-21(37)12-18)34-41(3,39)40/h4-15,17,34,37H,1-3H3,(H2,29,30,31,32)/t17-/m0/s1
Release date: 2018-11-07
CASP8 isoform G DED domain (PDB entry 7LVJ)
Macromolecule: Isoform 9 of Caspase-8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.61
Sequence length: 257 residues
Sequence: MSLEGGRRARVVIESKRNFFLGAFPTPFPAEHVELGRLGDSETAMVPGKGGADYILLPFKKMDFSRNLYDIGEQLDSEDLASLKFLSLDYIPQRKQEPIKDALMLFQRLQEKRMLEESNLSFLKELLFRINRLDLLITYLNTRKEEMERELQTPGRAQISAYRVMLYQISEEVSRSELRSFKALLQEEDSKCKLDDDMNLLDIFIEMEKRVILGEGKLDILKRVCAQINKSLLKIINDYEEFSKERSSSEGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1977
R free: 0.23
Average B factor: 23.198
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 281
Crystal growth procedure: 20% PEG 3350, 200mM Potassium Sodium Tartrate tetrahydrate
Matthews coefficient: 1.96
Solvent content (%): 37.22
Release date: 2022-03-02
Crystal structure of Dot1L in complex with inhibitor CPD5 [N-(2,6-dichlorophenyl)-4-methoxy-N-methylquinolin-6-amine] (PDB entry 5DTR)
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): 2.34
R work: 0.1727
R free: 0.2104
Average B factor: 56.64
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 1.2M K/Na tartrate, 0.1M Hepes pH6.6
Matthews coefficient: 3.48
Solvent content (%): 64.69
Ligand: N-(2,6-dichlorophenyl)-4-methoxy-N-methylquinolin-6-amine (5F7)
Ligand formula: C17 H14 Cl2 N2 O
Ligand molecular weight: 333.212
Ligand SMILES: CN(c1ccc2c(c1)c(ccn2)OC)c3c(cccc3Cl)Cl
Ligand InChI: InChI=1S/C17H14Cl2N2O/c1-21(17-13(18)4-3-5-14(17)19)11-6-7-15-12(10-11)16(22-2)8-9-20-15/h3-10H,1-2H3
Release date: 2016-06-15
Aurora A Kinase in Complex with ATP in Space Group P6122 (PDB entry 5DRD)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 273 residues
Sequence: MGRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRATLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.20592
R free: 0.26163
Average B factor: 59.809
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 292
Crystal growth procedure: 100 mM HEPES pH 7.4, 200 mM magnesium sulfate, 2-20% PEG3350
Matthews coefficient: 2.66
Solvent content (%): 53.74
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: 2016-07-20
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000625a (PDB entry 7GTN)
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): 1.66
R work: 0.1991
R free: 0.2293
Average B factor: 37.077
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.34
Solvent content (%): 63.17
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
Crystal structure of the T337M variant of human PGM-1 (PDB entry 7S0W)
Macromolecule: Phosphoglucomutase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.4.2.2
Sequence length: 585 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNMVKIVTVKTQAYQDQKPGTSGLRKRVKVFQSSANYAENFIQSIISTVEPAQRQEATLVVGGDGRFYMKEAIQLIARIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNPGGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAVCPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATMLRSIFDFSALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPMSGALDRVASATKIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQSVEDILKDHWQKYGRNFFTRYDYEEVEAEGANKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYSDPVDGSISRNQGLRLIFTDGSRIVFRLSGTGSAGATIRLYIDSYEKDVAKINQDPQVMLAPLISIALKVSQLQERTGRTAPTVIT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2145
R free: 0.2696
Average B factor: 78.14
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 1.8 M ammonium sulfate, 0.1 M MES, pH 6.5, 0.01 cobalt chloride
Matthews coefficient: 3.07
Solvent content (%): 59.91
Ligand: COBALT (II) ION (CO)
Ligand formula: Co
Ligand molecular weight: 58.933
Ligand SMILES: [Co+2]
Ligand InChI: InChI=1S/Co/q+2
Release date: 2022-05-04
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000069a (PDB entry 5QDK)
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): 1.555
R work: 0.1851
R free: 0.2096
Average B factor: 37.6971
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 (%): 63.19
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2018-10-10
X-ray structure of the complex between human alpha thrombin and NU172, a duplex/quadruplex 26-mer DNA aptamer, in the presence of potassium ions. (PDB entry 6EVV)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1691
R free: 0.2054
Average B factor: 48.197
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: Tacsimate 50 % v/v, pH 7.0
Matthews coefficient: 4.81
Solvent content (%): 74.41
Ligand: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide (0G6)
Ligand formula: C21 H34 Cl N6 O3
Ligand molecular weight: 453.986
Ligand SMILES: c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NC(CCCNC(=[NH2+])N)C(CCl)O)N
Ligand InChI: InChI=1S/C21H33ClN6O3/c22-13-18(29)16(8-4-10-26-21(24)25)27-19(30)17-9-5-11-28(17)20(31)15(23)12-14-6-2-1-3-7-14/h1-3,6-7,15-18,29H,4-5,8-13,23H2,(H,27,30)(H4,24,25,26)/p+1/t15-,16+,17+,18-/m1/s1
Release date: 2018-10-24
Crystal structure of TYK2 with Compound 11 (PDB entry 6X8F)
Macromolecule: Non-receptor tyrosine-protein kinase TYK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 318 residues
Sequence: MAHHHHHHHHHHGALEVLFQGPGDPTVFHKRYLKKIRDLGEGHFGKVSLYCYDPTNDGTGEMVAVKALKADAGPQHRSGWKQEIDILRTLYHEHIIKYKGCCEDAGAASLQLVMEYVPLGSLRDYLPRHSIGLAQLLLFAQQICEGMAYLHSQHYIHRDLAARNVLLDNDRLVKIGDFGLAKAVPEGHEYYRVREDGDSPVFWYAPECLKEYKFYYASDVWSFGVTLYELLTHCDSSQSPPTKFLELIGIAQGQMTVLRLTELLERGERLPRPDKCPAEVYHLMKNCWETEASFRPTFENLIPILKTVHEKYQGQAPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.2052
R free: 0.2549
Average B factor: 41.27
Crystallization method: EVAPORATION
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M bis-tris pH 5.5, 0.25 M NaCl, 10 mM TCEP, 27-33% PEG-3350
Matthews coefficient: 1.84
Solvent content (%): 33.09
Ligand: [3-{4-[6-(1-methyl-1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrazin-4-yl]-1H-pyrazol-1-yl}-1-(2,2,2-trifluoroethyl)azetidin-3-yl]acetonitrile (UWP)
Ligand formula: C20 H18 F3 N9
Ligand molecular weight: 441.412
Ligand SMILES: Cn1cc(cn1)c2cn3c(ccn3)c(n2)c4cnn(c4)C5(CN(C5)CC(F)(F)F)CC#N
Ligand InChI: InChI=1S/C20H18F3N9/c1-29-8-14(6-26-29)16-10-31-17(2-5-25-31)18(28-16)15-7-27-32(9-15)19(3-4-24)11-30(12-19)13-20(21,22)23/h2,5-10H,3,11-13H2,1H3
Release date: 2020-11-25
Human CAMKK2 with GSK650393 (PDB entry 6CMJ)
Macromolecule: Calcium/calmodulin-dependent protein kinase kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 321 residues
Sequence: MNAHHHHHHGSAENLYFQGHHVSITGMQDCVQLDQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNTVGTPAFMAPESLSETRKIFSGKALDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTRHGAEPLPSEDENCTLVE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1819
R free: 0.2192
Average B factor: 43.869
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 4 M sodium formate, 3% PEG8000, 20 mM ammonium sulfate
Matthews coefficient: 2.88
Solvent content (%): 57.26
Ligand: 2-(2-methylpropyl)-4-(5-phenyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzoic acid (F6J)
Ligand formula: C24 H22 N2 O2
Ligand molecular weight: 370.444
Ligand SMILES: CC(C)Cc1cc(ccc1C(=O)O)c2c[nH]c3c2cc(cn3)c4ccccc4
Ligand InChI: InChI=1S/C24H22N2O2/c1-15(2)10-18-11-17(8-9-20(18)24(27)28)22-14-26-23-21(22)12-19(13-25-23)16-6-4-3-5-7-16/h3-9,11-15H,10H2,1-2H3,(H,25,26)(H,27,28)
Release date: 2018-04-04
X-ray structure of NSD3-PWWP1 (PDB entry 6G3T)
Macromolecule: Histone-lysine N-methyltransferase NSD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 153 residues
Sequence: GEAPVQPILSSVPTTEVSTGVKFQVGDLVWSKVGTYPWWPCMVSSDPQLEVHTKINTRGAREYHVQFFSNQPERAWVHEKRVREYKGHKQYEELLAEATKQASNHSEKQKIRKPRPQRERAQWDIGIAHAEKALKMTREERIEQYTFIYIDKQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.229
R free: 0.274
Average B factor: 53.46
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM HEPES pH 7.8, 28% PEG3350, 2% PEG200, 1.5% 1,2-Butandiol
Matthews coefficient: 2.84
Solvent content (%): 56.67
Ligand: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE)
Ligand formula: C8 H18 N2 O4 S
Ligand molecular weight: 238.305
Ligand SMILES: C1CN(CCN1CCO)CCS(=O)(=O)O
Ligand InChI: InChI=1S/C8H18N2O4S/c11-7-5-9-1-3-10(4-2-9)6-8-15(12,13)14/h11H,1-8H2,(H,12,13,14)
Release date: 2019-06-26
Human Butyrylcholinesterase in complex with 2-(N-hydroxyimino)-N-[(1S)-3-{4-[(2-methyl-1H-imidazol-1-yl)methyl]-1H-1,2,3-triazol-1-yl}-1- phenylpropyl]acetamide (PDB entry 6T9S)
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): 2.7
R work: 0.2091
R free: 0.2446
Average B factor: 72.16
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate
Matthews coefficient: 3.17
Solvent content (%): 61.21
Ligand: (2~{E})-2-hydroxyimino-~{N}-[(1~{S})-3-[4-[(2-methylimidazol-1-yl)methyl]-1,2,3-triazol-1-yl]-1-phenyl-propyl]ethanamid
e (MXK)
Ligand formula: C18 H21 N7 O2
Ligand molecular weight: 367.405
Ligand SMILES: Cc1nccn1Cc2cn(nn2)CCC(c3ccccc3)NC(=O)C=NO
Ligand InChI: InChI=1S/C18H21N7O2/c1-14-19-8-10-24(14)12-16-13-25(23-22-16)9-7-17(21-18(26)11-20-27)15-5-3-2-4-6-15/h2-6,8,10-11,13,17,27H,7,9,12H2,1H3,(H,21,26)/b20-11+/t17-/m0/s1
Release date: 2020-07-15
Crystal structure of FGFR1-Y563C (FGFR4 surrogate) covalently bound to compound 11. (PDB entry 6P69)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: GAGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVECASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.18576
R free: 0.24498
Average B factor: 34.094
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 1:1 mix of protein + reservoir
Protein at ~15 mg/mL formulated in: 20mM Tris pH 8, 20mM NaCl, 2mM TCEP
Reservoir:
14-18% PEG 10K
0.3 M (NH4)2SO4
0.1 M MES pH 6.5
5% ethylene glycol
Matthews coefficient: 2.7
Solvent content (%): 54.51
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: 2019-06-19
Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 17: N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine (PDB entry 5VSE)
Macromolecule: Histone-lysine N-methyltransferase EHMT2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 275 residues
Sequence: TRTEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDNKDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQSRLA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1675
R free: 0.1906
Average B factor: 38.6584
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 290
Crystal growth procedure: 20 % PEG3350, 10% glycerol, 0.2 M Sodium fluoride, Bis-Tris propane pH6.5
Matthews coefficient: 2.54
Solvent content (%): 51.64
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: 2017-07-19
The crystal structure of human abl1 kinase domain in complex with abl1-B-EBA (PDB entry 8H7F)
Macromolecule: Tyrosine-protein kinase ABL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 277 residues
Sequence: GAMGSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4501342407
R work: 0.203775710345
R free: 0.234153850318
Average B factor: 39.8427698956
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.5M (NH4)2 SO4, 0.1M HEPES (PH 7.0) and 4% v/v 1,3-Propanediol.
Matthews coefficient: 3.11
Solvent content (%): 60.46
Ligand: 1-[6-(6-methoxyisoquinolin-7-yl)-1,3-benzothiazol-2-yl]-3-(2-oxidanylideneethyl)urea (QEW)
Ligand formula: C20 H16 N4 O3 S
Ligand molecular weight: 392.431
Ligand SMILES: COc1cc2ccncc2cc1c3ccc4c(c3)sc(n4)NC(=O)NCC=O
Ligand InChI: InChI=1S/C20H16N4O3S/c1-27-17-9-12-4-5-21-11-14(12)8-15(17)13-2-3-16-18(10-13)28-20(23-16)24-19(26)22-6-7-25/h2-5,7-11H,6H2,1H3,(H2,22,23,24,26)
Release date: 2023-03-01
Crystal structure of KDM3B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol (PDB entry 6RBJ)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 351 residues
Sequence: SMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKQRIHDGKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.093
R work: 0.1889
R free: 0.2103
Average B factor: 43.1198
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M bis-tris pH 6.6 , 0.1 M magnesium chloride, 28% PEG 3350
Matthews coefficient: 2.88
Solvent content (%): 57.3
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: 2020-05-13