satarupa22/MacromolecularLigandDB huggingface dataset:
Bromodomain of CBP liganded with iCBP6 (PDB entry 8FXE)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.156
R free: 0.1864
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.2 M Sodium chloride, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3350
Matthews coefficient: 2.51
Solvent content (%): 51.08
Ligand: (6S)-1-(3-tert-butylphenyl)-6-{(5P)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1s,4R)-4-methoxycyclohexyl]-1H-benzimidazol-2-yl}piperidin-2-one (YID)
Ligand formula: C34 H42 N4 O3
Ligand molecular weight: 554.722
Ligand SMILES: Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)OC)C5CCCC(=O)N5c6cccc(c6)C(C)(C)C
Ligand InChI: InChI=1S/C34H42N4O3/c1-21-32(22(2)41-36-21)23-13-18-29-28(19-23)35-33(38(29)25-14-16-27(40-6)17-15-25)30-11-8-12-31(39)37(30)26-10-7-9-24(20-26)34(3,4)5/h7,9-10,13,18-20,25,27,30H,8,11-12,14-17H2,1-6H3/t25-,27+,30-/m0/s1
Release date: 2024-02-07
Notum Fragment 282 (PDB entry 7B98)
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): 1.53
R work: 0.2089
R free: 0.2354
Average B factor: 24.8108
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.99
Solvent content (%): 38.28
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 TNKS2 in complex with 2-(2,4-dichlorophenyl)-1- methyl-1H,2H,3H,4H-pyrido(2,3-d)pyrimidin-4-one (PDB entry 5AL3)
Macromolecule: TANKYRASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 240 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.15873
R free: 0.19309
Average B factor: 26.239
Crystallization pH: 8.5
Crystal growth procedure: pH 8.5
Matthews coefficient: 2.4
Solvent content (%): 49
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: 2015-07-29
Truncated mitofusin-1, GTP-bound (PDB entry 5GOF)
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): 1.604
R work: 0.1793
R free: 0.2145
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1mM ZnCl2, 100mM Tris-HCl (pH 8.0~9.0), 15~16% PEG 3350, 10~15% glycerol
Matthews coefficient: 2.74
Solvent content (%): 55.11
Ligand: GUANOSINE-5'-TRIPHOSPHATE (GTP)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2017-01-25
Crystal structures and ribonuclease activity of the Flavivirus host factor ERI3 that is involved in viral RNA synthesis define the ERI subfamily of structure-specific 3-prime - 5-prime exoribonucleases (PDB entry 7LPY)
Macromolecule: ERI1 exoribonuclease 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 216 residues
Sequence: MHHHHHHENLYFQSMSFPPQRYHYFLVLDFEATCDKPQIHPQEIIEFPILKLNGRTMEIESTFHMYVQPVVHPQLTPFCTELTGIIQAMVDGQPSLQQVLERVDEWMAKEGLLDPNVKSIFVTCGDWDLKVMLPGQCQYLGLPVADYFKQWINLKKAYSFAMGCWPKNGLLDMNKGLSLQHIGRPHSGIDDCKNIANIMKTLAYRGFIFKQTSKPF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1789
R free: 0.2051
Average B factor: 57.81
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 35% PEG 3350,
20% saturated KCl,
200 mM Imidazole / Malate buffer pH 8.0,
5mM MnCl2,
18mM AMP,
3.3 mM N-{2-[4-(thiophen-2-yl)-1H-imidazol-2-yl]ethyl}-2,3-dihydro-1,4-benzodioxine-2-carboxamide (from Life Chemicals)
Matthews coefficient: 2.11
Solvent content (%): 41.64
Ligand: ADENOSINE MONOPHOSPHATE (AMP)
Ligand formula: C10 H14 N5 O7 P
Ligand molecular weight: 347.221
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2022-02-16
UCHL3 in complex with synthetic, K27-linked diubiquitin (PDB entry 6QML)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase isozyme L3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 227 residues
Sequence: QRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1843
R free: 0.2332
Average B factor: 55.422
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298.15
Crystal growth procedure: Drops set up in MRC 2 well, 96 well plate using a Mosquito crystallization robot. 100+100 nl drops.
Best crystals:
21% PEG 3350
0.15M KBr
0.1M Bis-Tris pH 5.5

Crystals grow also in KCl and AmSO4 (0.2 M), or with PEG 200 MME. Crystals can be obtained at 4C as well.
Matthews coefficient: 2.67
Solvent content (%): 54.04
Ligand: POTASSIUM ION (K)
Ligand formula: K
Ligand molecular weight: 39.098
Ligand SMILES: [K+]
Ligand InChI: InChI=1S/K/q+1
Release date: 2020-02-26
Human butyrylcholinesterase in complex with 2,2'-(((1E,1'E)-(2-phenylpyrimidine-4,6-diyl)bis(methaneylylidene))bis(hydrazin-1-yl-2-ylidene))bis(N,N,N-trimethyl-2-oxoethan-1-aminium) (PDB entry 8AM2)
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): 2.5
R work: 0.1702
R free: 0.2198
Average B factor: 53.41
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: AMMONIUM SULFATE 2.1 M, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID 0.1 M
Matthews coefficient: 3.22
Solvent content (%): 61.75
Ligand: ~{N}-[(~{E})-[2-phenyl-6-[[2-[2-(trimethyl-$l^{4}-azanyl)ethanoyl]hydrazinyl]methyl]pyrimidin-4-yl]methylideneamino]-2-(trimethyl-$l^{4}-azanyl)ethanamide (N0C)
Ligand formula: C22 H34 N8 O2
Ligand molecular weight: 442.558
Ligand SMILES: C[N+](C)(C)CC(=O)NNCc1cc(nc(n1)c2ccccc2)C=NNC(=O)C[N+](C)(C)C
Ligand InChI: InChI=1S/C22H32N8O2/c1-29(2,3)15-20(31)27-23-13-18-12-19(14-24-28-21(32)16-30(4,5)6)26-22(25-18)17-10-8-7-9-11-17/h7-13H,14-16H2,1-6H3,(H-2,23,24,25,26,27,28,31,32)/p+2
Release date: 2023-06-14
CRYSTAL STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2-WT) COMPLEX WITH N-[5-[[[5-(1,1-DIMETHYLETHYL)-2-OXAZOLYL] METHYL]THIO]-2-THIAZOLYL]-4-PIPERIDINECARBOXAMIDE (BMS-387032) (PDB entry 5D1J)
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): 1.8
R work: 0.2013
R free: 0.2322
Average B factor: 35.56
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 316
Crystal growth procedure: 35% poly(ethylene glycol) 5000 monomethyl ester, 0.2 M ammonium acetate, 0.1 M HEPES, pH 7.0,
Matthews coefficient: 2.09
Solvent content (%): 41.06
Ligand: N-(5-{[(5-tert-butyl-1,3-oxazol-2-yl)methyl]sulfanyl}-1,3-thiazol-2-yl)piperidine-4-carboxamide (56H)
Ligand formula: C17 H24 N4 O2 S2
Ligand molecular weight: 380.528
Ligand SMILES: CC(C)(C)c1cnc(o1)CSc2cnc(s2)NC(=O)C3CCNCC3
Ligand InChI: InChI=1S/C17H24N4O2S2/c1-17(2,3)12-8-19-13(23-12)10-24-14-9-20-16(25-14)21-15(22)11-4-6-18-7-5-11/h8-9,11,18H,4-7,10H2,1-3H3,(H,20,21,22)
Release date: 2015-08-12
Crystal Structure of BACE1 in complex with N-{3-[(9S)-7-amino-2,2-difluoro-9-(prop-1-yn-1-yl)-6-oxa-8-azaspiro[3.5]non-7-en-9-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide (PDB entry 7D5A)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 416 residues
Sequence: GSHMLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2069
R free: 0.2424
Average B factor: 35.923
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M sodium citrate tribasic pH6.5, 0.2 M ammonium iodide, 18% w/v PEG 5000MME
Matthews coefficient: 2.76
Solvent content (%): 55.39
Ligand: N-[3-[(9S)-7-azanyl-2,2-bis(fluoranyl)-9-prop-1-ynyl-6-oxa-8-azaspiro[3.5]non-7-en-9-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide (GX6)
Ligand formula: C23 H18 F3 N5 O2
Ligand molecular weight: 453.417
Ligand SMILES: CC#CC1(C2(CC(C2)(F)F)COC(=N1)N)c3cc(ccc3F)NC(=O)c4ccc(cn4)C#N
Ligand InChI: InChI=1S/C23H18F3N5O2/c1-2-7-23(21(11-22(25,26)12-21)13-33-20(28)31-23)16-8-15(4-5-17(16)24)30-19(32)18-6-3-14(9-27)10-29-18/h3-6,8,10H,11-13H2,1H3,(H2,28,31)(H,30,32)/t23-/m1/s1
Release date: 2021-03-31
Crystal structure of the BRAF (R509H) kinase domain monomer bound to Vemurafenib (PDB entry 4RZV)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 281 residues
Sequence: RRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTHHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.994
R work: 0.2042
R free: 0.2671
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris pH 7.0, 18% (w/v) PEG2000 MME , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Matthews coefficient: 2.21
Solvent content (%): 44.41
Ligand: N-(3-{[5-(4-chlorophenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]carbonyl}-2,4-difluorophenyl)propane-1-sulfonamide (032)
Ligand formula: C23 H18 Cl F2 N3 O3 S
Ligand molecular weight: 489.922
Ligand SMILES: CCCS(=O)(=O)Nc1ccc(c(c1F)C(=O)c2c[nH]c3c2cc(cn3)c4ccc(cc4)Cl)F
Ligand InChI: InChI=1S/C23H18ClF2N3O3S/c1-2-9-33(31,32)29-19-8-7-18(25)20(21(19)26)22(30)17-12-28-23-16(17)10-14(11-27-23)13-3-5-15(24)6-4-13/h3-8,10-12,29H,2,9H2,1H3,(H,27,28)
Release date: 2016-08-10
Crystal structure of Rev7-WT/Rev3 as a monomer under high-salt conditions (PDB entry 6BI7)
Macromolecule: Mitotic spindle assembly checkpoint protein MAD2B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 227 residues
Sequence: MGSSHHHHHHSQDPNSMTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLRAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKGS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2754
R free: 0.3213
Average B factor: 94.6819
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289.15
Crystal growth procedure: hRev7/3 at 60 mg/mL in 5 mM HEPES, 100 mM NaCl, 10 mM DTT, pH=7.4 was mixed in a 1:1 ratio with a well solution consisting of 100 mM sodium citrate, 1M LiCl, 7.5% (w/v) PEG6000 at pH=4.75. Crystals were frozen in the reservoir solution with the addition of 20% (w/v) sucrose
Matthews coefficient: 2.81
Solvent content (%): 56.17
Release date: 2018-08-01
EGFR kinase domain mutant "TMLR" with pyridone compound 2: 4-[2-(4-chlorophenyl)ethylamino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide (PDB entry 5EM5)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2123
R free: 0.2229
Average B factor: 67.33
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: PEG 10K, ethylene glycol
Matthews coefficient: 3.67
Solvent content (%): 66.47
Ligand: 4-[2-(4-chlorophenyl)ethylamino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide (5Q2)
Ligand formula: C25 H28 Cl N5 O2
Ligand molecular weight: 465.975
Ligand SMILES: CN1CCN(CC1)c2ccc(cc2)NC(=O)C3=C(C=CNC3=O)NCCc4ccc(cc4)Cl
Ligand InChI: InChI=1S/C25H28ClN5O2/c1-30-14-16-31(17-15-30)21-8-6-20(7-9-21)29-25(33)23-22(11-13-28-24(23)32)27-12-10-18-2-4-19(26)5-3-18/h2-9,11,13H,10,12,14-17H2,1H3,(H,29,33)(H2,27,28,32)
Release date: 2015-12-30
Apo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I) (PDB entry 8UC5)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 166 residues
Sequence: SNANPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1442
R free: 0.1754
Average B factor: 18.71
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: Well solution: 2.1 M DL-Malic acid pH 7.0.
Protein solution: 15 mg/mL protein, 20 mM Tris pH 8.0, 50 mM NaCl, 1 mM DTT, and 5% glycerol.
Drop: 1 uL protein, 1 uL well solution
Matthews coefficient: 2.78
Solvent content (%): 55.73
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: 2024-09-04
MELK in complex with NVS-MELK5 (PDB entry 5K00)
Macromolecule: Maternal embryonic leucine zipper kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 335 residues
Sequence: MDYDELLKYYELHETIGTGGFAKVKLACHILTGEMVAIKIMDKNTLGSDLPRIKTEIEALKNLRHQHICQLYHVLETANKIFMVLEYCPGGELFDYIISQDRLSEEETRVVFRQIVSAVAYVHSQGYAHRDLKPENLLFDEYHKLKLIDFGLCAKPKGNKDYHLQTCCGSLAYAAPELIQGKSYLGSEADVWSMGILLYVLMCGFLPFDDDNVMALYKKIMRGKYDVPKWLSPSSILLLQQMLQVDPKKRISMKNLLNHPWIMQDYNYPVEWQSKNPFIHLDDDCVTELSVHHRNNRQTMEDLISLWQYDHLTATYLLLLAKKARGKPVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.1742
R free: 0.1955
Average B factor: 38.41
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 100mM Hepes pH 7.6, 0.2M NaCl, 13.3% PEG 3350
Matthews coefficient: 2.6
Solvent content (%): 52.71
Ligand: 4-{2-[(3-methoxyphenyl)amino]-4-[(piperidin-4-yl)methoxy]pyrimidin-5-yl}-N-[2-oxo-2-(phenylamino)ethyl]benzamide (6PV)
Ligand formula: C32 H34 N6 O4
Ligand molecular weight: 566.65
Ligand SMILES: COc1cccc(c1)Nc2ncc(c(n2)OCC3CCNCC3)c4ccc(cc4)C(=O)NCC(=O)Nc5ccccc5
Ligand InChI: InChI=1S/C32H34N6O4/c1-41-27-9-5-8-26(18-27)37-32-35-19-28(31(38-32)42-21-22-14-16-33-17-15-22)23-10-12-24(13-11-23)30(40)34-20-29(39)36-25-6-3-2-4-7-25/h2-13,18-19,22,33H,14-17,20-21H2,1H3,(H,34,40)(H,36,39)(H,35,37,38)
Release date: 2017-03-01
Crystal structure of human ATAD2 bromodomain in complex with 8-(3R,4R) -3-(cyclohexylmethoxy)piperidin-4-yl-amino-3-methyl-1,2-dihydro-1,7- naphthyridin-2-one (PDB entry 5A81)
Macromolecule: ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.19659
R free: 0.21938
Average B factor: 32.306
Matthews coefficient: 4.08
Solvent content (%): 69.88
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: 2015-08-12
Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 60 s (PDB entry 5VRZ)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG)P*GP*CP*GP*CP*AP*TP*CP*AP*G)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACAGGCGCATCAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1968
R free: 0.2417
Average B factor: 30.666
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
Matthews coefficient: 2.23
Solvent content (%): 44.74
Ligand: THYMIDINE-5'-TRIPHOSPHATE (TTP)
Ligand formula: C10 H17 N2 O14 P3
Ligand molecular weight: 482.168
Ligand SMILES: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
Release date: 2017-07-19
Crystal structure of human SHIP2 Phosphatase-C2 (PDB entry 5OKM)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 461 residues
Sequence: GPEPDMISVFIGTWNMGSVPPPKNVTSWFTSKGLGKTLDEVTVTIPHDIYVFGTQENSVGDREWLDLLRGGLKELTDLDYRPIAMQSLWNIKVAVLVKPEHENRISHVSTSSVKTGIANTLGNKGAVGVSFMFNGTSFGFVNCHLTSGNEKTARRNQNYLDILRLLSLGDRQLNAFDISLRFTHLFWFGDLNYRLDMDIQEILNYISRKEFEPLLRVDQLNLEREKHKVFLRFSEEEISFPPTYRYERGSRDTYAWHKQKPTGVRTNVPSWCDRILWKSYPETHIICNSYGCTDDIVTSDHSPVFGTFEVGVTSQFISKKGLSKTSDQAYIEFESIEAIVKTASRTKFFIEFYSTCLEEYKKSFENDAQSSDNINFLKVQWSSRQLPTLKPILADIEYLQDQHLLLTVKSMDGYESYGECVVALKSMIGSTAQQFLTFLSHRGEETGNIRGSMKVRVPTER
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1795
R free: 0.2075
Average B factor: 45.654
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M BisTris propane pH 7, 0.2 M NaNO3, 20% PEG 3350, 0.025% CH2Cl2, 2 mM TCEP
Matthews coefficient: 2.54
Solvent content (%): 51.66
Ligand: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (B3P)
Ligand formula: C11 H26 N2 O6
Ligand molecular weight: 282.334
Ligand SMILES: C(CNC(CO)(CO)CO)CNC(CO)(CO)CO
Ligand InChI: InChI=1S/C11H26N2O6/c14-4-10(5-15,6-16)12-2-1-3-13-11(7-17,8-18)9-19/h12-19H,1-9H2
Release date: 2017-08-23
CRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5 (STEP) IN COMPLEX WITH COMPOUND 2 (PDB entry 6H8R)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 305 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSRVLQAEELHEKALDPFLLQAEFFEIPMNFVDPKEYDIPGLVRKNRYKTILPNPHSRVCLTSPDPDDPLSSYINANYIRGYGGEEKVYIATQGPIVSTVADFWRMVWQEHTPIIVMITNIEEMNEKCTEYWPEEQVAYDGVEITVQKVIHTEDYRLRLISLKSGTEERGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQQEGPHCAPIIVHCSAGIGRTGCFIATSICCQQLRQEGVVDILKTTCQLRQDRGGMIQTCEQYQFVHHVMSLYEKQLSHQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.2
R free: 0.239
Average B factor: 25.36
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 24 % PEG 3350, 0.2 M ammonium sulfate and 0.1 M BIS-Tris pH 5.5
Matthews coefficient: 2.59
Solvent content (%): 52.43
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: 2018-09-26