satarupa22/MacromolecularLigandDB huggingface dataset:
Human Cyclophilin D in complex with 1-(((2R,3S,6R)-3-hydroxy-2,3,4,6-tetrahydro-1H-2,6-methanobenzo[c][1,5]oxazocin-8-yl)methyl)-3-(2-((R)-2-(2-(methylthio)phenyl)pyrrolidin-1-yl)-2-oxoethyl)urea (PDB entry 6R8O)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.36
R work: 0.143
R free: 0.182
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: PEG 3350
Matthews coefficient: 2.6
Solvent content (%): 52.7
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: 2019-11-27
Crystal structure of KAT6A in complex with inhibitor CTx-648 (PF-9363) (PDB entry 8DD5)
Macromolecule: Histone acetyltransferase KAT6A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 286 residues
Sequence: GSPPDPQVRCPSVIEFGKYEIHTWYSSPYPQEYSRLPKLYLCEFCLKYMKSRTILQQHMKKCGWFHPPANEIYRKNNISVFEVDGNVSTIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVLTQNDVKGCHLVGYFSKEKHCQQKYNVSCIMILPQYQRKGYGRFLIDFSYLLSKREGQAGSPEKPLSDLGRLSYMAYWKSVILECLYHQNDKQISIKKLSKLTGICPQDITSTLHHLRMLDFRSDQFVIIRREKLIQDHMAKLQLNLRPVDVDPECLRWTPVIVSNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58
R work: 0.232
R free: 0.263
Average B factor: 79.44
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM sodium chloride
100 mM HEPES (pH 6.64)
1.8 M ammonium sulfate
Matthews coefficient: 2.77
Solvent content (%): 55.53
Ligand: 2,6-dimethoxy-N-{4-methoxy-6-[(1H-pyrazol-1-yl)methyl]-1,2-benzoxazol-3-yl}benzene-1-sulfonamide (R7L)
Ligand formula: C20 H20 N4 O6 S
Ligand molecular weight: 444.461
Ligand SMILES: COc1cccc(c1S(=O)(=O)Nc2c3c(cc(cc3OC)Cn4cccn4)on2)OC
Ligand InChI: InChI=1S/C20H20N4O6S/c1-27-14-6-4-7-15(28-2)19(14)31(25,26)23-20-18-16(29-3)10-13(11-17(18)30-22-20)12-24-9-5-8-21-24/h4-11H,12H2,1-3H3,(H,22,23)
Release date: 2023-07-05
Structure of human dihydroorotate dehydrogenase in complex with 280-12 (PDB entry 5ZF9)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 390 residues
Sequence: MGHHHHHHHHHHSSGHIDDDDKHMATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.16312
R free: 0.18124
Average B factor: 20.216
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.9
Crystallization temperature (K): 293
Crystal growth procedure: 100MM SODIUM ACETATE, 1.8-1.9M AMMONIUM SULPHATE, 40MM C11DAO, 20.8MM DDAO, 2MM DIHYDROOROTATE
Matthews coefficient: 3.41
Solvent content (%): 63.96
Ligand: OROTIC ACID (ORO)
Ligand formula: C5 H4 N2 O4
Ligand molecular weight: 156.096
Ligand SMILES: C1=C(NC(=O)NC1=O)C(=O)O
Ligand InChI: InChI=1S/C5H4N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h1H,(H,9,10)(H2,6,7,8,11)
Release date: 2018-09-26
Crystal structure of human Cathepsin-S with bound ligand (PDB entry 5QCA)
Macromolecule: Cathepsin S
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.27
Sequence length: 223 residues
Sequence: ILPDSVDWREKGCVTEVKYQGSCGASWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEILQGGG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29
R work: 0.178
R free: 0.217
Average B factor: 26.14
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Matthews coefficient: 2.72
Solvent content (%): 54.72
Ligand: 1-{4-[(2-chloro-5-{1-[3-(4-cyclopropylpiperazin-1-yl)propyl]-5-(methylsulfonyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-3-yl}phenyl)ethynyl]phenyl}-N-[(4-chlorophenyl)methyl]methanamine (BGJ)
Ligand formula: C39 H44 Cl2 N6 O2 S
Ligand molecular weight: 731.777
Ligand SMILES: CS(=O)(=O)N1CCc2c(c(nn2CCCN3CCN(CC3)C4CC4)c5ccc(c(c5)C#Cc6ccc(cc6)CNCc7ccc(cc7)Cl)Cl)C1
Ligand InChI: InChI=1S/C39H44Cl2N6O2S/c1-50(48,49)46-20-17-38-36(28-46)39(43-47(38)19-2-18-44-21-23-45(24-22-44)35-14-15-35)33-11-16-37(41)32(25-33)10-7-29-3-5-30(6-4-29)26-42-27-31-8-12-34(40)13-9-31/h3-6,8-9,11-13,16,25,35,42H,2,14-15,17-24,26-28H2,1H3
Release date: 2017-12-20
COMPLEMENT FACTOR D IN COMPLEX WITH A REVERSIBLE BENZOIC ACID BASED INHIBITOR (PDB entry 5MT4)
Macromolecule: Complement factor D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.46
Sequence length: 232 residues
Sequence: ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLASAAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.19
R free: 0.239
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 26% PEGME2000, 100mM Bis-Tris pH 6.5
Matthews coefficient: 2.17
Solvent content (%): 43.27
Ligand: 2-[(phenylmethyl)carbamoylamino]benzoic acid (M7O)
Ligand formula: C15 H14 N2 O3
Ligand molecular weight: 270.283
Ligand SMILES: c1ccc(cc1)CNC(=O)Nc2ccccc2C(=O)O
Ligand InChI: InChI=1S/C15H14N2O3/c18-14(19)12-8-4-5-9-13(12)17-15(20)16-10-11-6-2-1-3-7-11/h1-9H,10H2,(H,18,19)(H2,16,17,20)
Release date: 2017-02-15
Human Carbonic Anhydrase II native 00 atm CO2 (PDB entry 6KM3)
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): 1.15
R work: 0.1036
R free: 0.1278
Average B factor: 13.117
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 100 mM Tris-HCl
Matthews coefficient: 2.07
Solvent content (%): 40.65
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-08-05
Crystal structure of human carbonic anhydrase isozyme II with N-butyl-2,4-dichloro-5-sulfamoyl-benzamide (PDB entry 6G6T)
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): 1.12
R work: 0.1433
R free: 0.1774
Average B factor: 16.1384
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M sodium bicine (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7)
Matthews coefficient: 2.07
Solvent content (%): 40.2
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: 2019-03-13
KRAS-G13D in complex with BI-2493 (PDB entry 8ONV)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGAGDVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.01
R work: 0.1336
R free: 0.1565
Average B factor: 20.14
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 0.2mM MgCl2, 15-27% PEG 2000, 100mM sodium acetate pH=4.4
Matthews coefficient: 2.53
Solvent content (%): 51.4
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: 2023-06-07
Human CA II in complex with benzyl alcohol (PDB entry 7BI5)
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): 1.74
R work: 0.1695
R free: 0.1938
Average B factor: 11.7522
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 0.1 M Tris-HCl
Matthews coefficient: 2.08
Solvent content (%): 40.94
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: 2021-03-17
Carbonic Anhydrase II in complex with the diaryl urea molecule J2 (PDB entry 8EM3)
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): 1.62
R work: 0.1528
R free: 0.1844
Average B factor: 22.9338
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.6M Sodium Citrate, 50mM Tris base
Matthews coefficient: 2.12
Solvent content (%): 42.03
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: 2023-09-27
Crystal structure of human carbonic anhydrase II in complex with the inhibitor famotidine (PDB entry 6G3Q)
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): 1.01
R work: 0.1271
R free: 0.1515
Average B factor: 17.115
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, Tris 50 mM
Matthews coefficient: 2.09
Solvent content (%): 41.19
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: 2018-11-28
Crystal structure of human Sirt2 in complex with a brominated 2nd generation SirReal inhibitor and NAD+ (PDB entry 5DY4)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 304 residues
Sequence: GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.17494
R free: 0.21286
Average B factor: 33.455
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 278
Crystal growth procedure: 27 % PEG 3350
Matthews coefficient: 2.96
Solvent content (%): 58.46
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-01-13
Notum Fragment 830 (PDB entry 7BD5)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.201
R free: 0.2327
Average B factor: 24.8058
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: .5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 2.01
Solvent content (%): 38.75
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: 2022-01-12
Crystal structure of JAK2 JH2 (pseudokinase domain) in complex with Reversine (PDB entry 8EX1)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1685
R free: 0.1905
Average B factor: 22.23
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: HEPES, PEG 3350
Matthews coefficient: 2.41
Solvent content (%): 49.05
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
The structure of the polo-box domain (PBD) of Plk1 in complex with Z228588490 (PDB entry 5NN2)
Macromolecule: Serine/threonine-protein kinase PLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.21
Sequence length: 232 residues
Sequence: GPLGSPEFDCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.1872
R free: 0.2186
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 200 mM K/Na Tartrate, 10-20% PEG3350
Matthews coefficient: 2.05
Solvent content (%): 40.1
Ligand: (3~{R},5~{R})-1-[2,4-bis(fluoranyl)phenyl]-5-oxidanyl-pyrrolidine-3-carboxylic acid (Z24)
Ligand formula: C11 H11 F2 N O3
Ligand molecular weight: 243.207
Ligand SMILES: c1cc(c(cc1F)F)N2CC(CC2O)C(=O)O
Ligand InChI: InChI=1S/C11H11F2NO3/c12-7-1-2-9(8(13)4-7)14-5-6(11(16)17)3-10(14)15/h1-2,4,6,10,15H,3,5H2,(H,16,17)/t6-,10-/m1/s1
Release date: 2018-02-21
Factor XIa in Complex with Compound 2a (PDB entry 7V0Z)
Macromolecule: Coagulation factor XIa light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 238 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1761
R free: 0.2024
Average B factor: 27.6547
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 4000, 100mM Na Citrate pH 5.0
Matthews coefficient: 2.24
Solvent content (%): 44.97
Ligand: methyl ~{N}-[4-[1-[(1~{R})-1-[5-[5-chloranyl-2-(1,2,3,4-tetrazol-1-yl)phenyl]-1-oxidanyl-pyridin-2-yl]-2-cyclopropyl-ethyl]pyrazol-4-yl]phenyl]carbamate (OQ6)
Ligand formula: C28 H25 Cl N8 O3
Ligand molecular weight: 557.003
Ligand SMILES: COC(=O)Nc1ccc(cc1)c2cnn(c2)C(CC3CC3)c4ccc(c[n+]4[O-])c5cc(ccc5n6cnnn6)Cl
Ligand InChI: InChI=1S/C28H25ClN8O3/c1-40-28(38)32-23-8-4-19(5-9-23)21-14-31-35(15-21)27(12-18-2-3-18)26-10-6-20(16-37(26)39)24-13-22(29)7-11-25(24)36-17-30-33-34-36/h4-11,13-18,27H,2-3,12H2,1H3,(H,32,38)/t27-/m1/s1
Release date: 2022-08-03
Human MBD4 glycosylase domain bound to DNA containing an abasic site (PDB entry 7KZ1)
Macromolecule: Methyl-CpG-binding domain protein 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 157 residues
Sequence: GSALSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62
R work: 0.1818
R free: 0.2054
Average B factor: 37.2099
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: PEG400, Tris-HCl
Matthews coefficient: 2.1
Solvent content (%): 41.55
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: 2021-11-10
The Crystal Structure of CDK3 and CyclinE1 Complex from Biortus. (PDB entry 7XQK)
Macromolecule: Glutathione S-transferase class-mu 26 kDa isozyme,Cyclin-dependent kinase 3
Type: Protein, polypeptide(L)
Source organism: Schistosoma japonicum
EC number: 2.5.1.18
Sequence length: 533 residues
Sequence: MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSDLEVLFQGPMDMFQKVEKIGEGTYGVVYKAKNRETGQLVALKKIRLDLEMEGVPSTAIREISLLKELKHPNIVRLLDVVHNERKLYLVFEFLSQDLKKYMDSTPGSELPLHLIKSYLFQLLQGVSFCHSHRVIHRDLKPQNLLINELGAIKLADFGLARAFGVPLRTYTHEVVTLWYRAPEILLGSKFYTTAVDIWSIGCIFAEMVTRKALFPGDSEIDQLFRIFRMLGTPSEDTWPGVTQLPDYKGSFPKWTRKGLEEIVPNLEPEGRDLLMQLLQYDPSQRITAKTALAHPYFSSPEPSPAARQYVLQRFRH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1599
R free: 0.2024
Average B factor: 38.105
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.6M MgSO4, 0.1M MES pH6.5
Matthews coefficient: 2.69
Solvent content (%): 54.35
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: 2023-05-17
Crystal Structure of the Human vaccinia-related kinase bound to a N-methyl-N-propyl-dihydropteridine inhibitor (PDB entry 6CSW)
Macromolecule: Serine/threonine-protein kinase VRK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.18757
R free: 0.23289
Average B factor: 35.987
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 27.5% PEG3350; 300 mM LiSO4; 0.1M SBG pH 7.0
Matthews coefficient: 2.59
Solvent content (%): 52.57
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: 2018-04-04
Crystal Structure of p38alpha in Complex with Lipid Pocket Ligand 9c (PDB entry 5N63)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1946
R free: 0.2282
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM MES pH 5.6-6.2,
20-30 % PEG4000
Matthews coefficient: 2.31
Solvent content (%): 46.78
Ligand: ~{N}4-[(4-fluorophenyl)methyl]-2-phenyl-quinazoline-4,7-diamine (8OW)
Ligand formula: C21 H17 F N4
Ligand molecular weight: 344.385
Ligand SMILES: c1ccc(cc1)c2nc3cc(ccc3c(n2)NCc4ccc(cc4)F)N
Ligand InChI: InChI=1S/C21H17FN4/c22-16-8-6-14(7-9-16)13-24-21-18-11-10-17(23)12-19(18)25-20(26-21)15-4-2-1-3-5-15/h1-12H,13,23H2,(H,24,25,26)
Release date: 2017-09-20