satarupa22/MacromolecularLigandDB huggingface dataset:
The molecular tweezer CLR01 stabilizes a disordered protein-protein interface (PDB entry 5M36)
Macromolecule: 14-3-3 protein zeta/delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 229 residues
Sequence: DKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTEGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEESYKDSTLIMQLLRDNLTLWTS
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.2238
R free: 0.2736
Average B factor: 77.665
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.17 M Ammonium acetate; 0.085 M Sodium citrate pH 5.6; 25.5% (w/v) PEG 4000; 15% (v/v) Glycerol
Matthews coefficient: 3.7
Solvent content (%): 66.72
Ligand: (1R,5S,9S,16R,20R,24S,28S,35R)-3,22-Bis(dihydroxyphosphoryloxy)tridecacyclo[22.14.1.15,20.19,16.128,35.02,23.04,21.06,19.08,17.010,15.025,38.027,36.029,34]dotetraconta-2(23),3,6,8(17),10,12,14,18,21,25,27(36),29,31,33,37-pentadecaene (9SZ)
Ligand formula: C42 H32 O8 P2
Ligand molecular weight: 726.646
Ligand SMILES: c1ccc2c(c1)C3CC2c4c3cc5c(c4)C6CC5c7c6c(c8c(c7OP(=O)(O)O)C9CC8c1c9cc2c(c1)C1CC2c2c1cccc2)OP(=O)(O)O
Ligand InChI: InChI=1S/C42H32O8P2/c43-51(44,45)49-41-37-33-15-34(30-12-26-22-9-21(25(26)11-29(30)33)17-5-1-2-6-18(17)22)38(37)42(50-52(46,47)48)40-36-16-35(39(40)41)31-13-27-23-10-24(28(27)14-32(31)36)20-8-4-3-7-19(20)23/h1-8,11-14,21-24,33-36H,9-10,15-16H2,(H2,43,44,45)(H2,46,47,48)/t21-,22+,23+,24-,33-,34+,35+,36-
Release date: 2017-11-15
Discovery of ASTX029, a clinical candidate which modulates the phosphorylation and catalytic activity of ERK1/2 (PDB entry 7NR5)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.766
R work: 0.1736
R free: 0.2226
Average B factor: 27.647
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.25M (NH4)2SO4
33% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.31
Solvent content (%): 46.82
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: 2021-10-06
Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+) and NADH (PDB entry 5YVT)
Macromolecule: Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.41
Sequence length: 339 residues
Sequence: TGGVQTVTLIPGDGIGPEISAAVMKIFDAAKAPIQWEERNVTAIQGPGGKWMIPSEAKESMDKNKMGLKGPLKTPIAAGHPSMNLLLRKTFDLYANVRPCVSIEGYKTPYTDVNIVTIRENTEGEYSGIEHVIVDGVVQSIKLITEGASKRIAEFAFEYARNNHRSNVTAVHKANIMRMSDGLFLQKCREVAESCKDIKFNEMYLDTVCLNMVQDPSQFDVLVMPNLYGDILSDLCAGLIGGLGVTPSGNIGANGVAIFESVHGTAPDIAGKDMANPTALLLSAVMMLRHMGLFDHAARIEAACFATIKDGKSLTKDLGGNAKCSDFTEEICRRVKDLD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.21136
R free: 0.23637
Average B factor: 64.145
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES-Na, pH 7.5, 50 mM MgCl2, 30% (v/v) PEGMME 550
Matthews coefficient: 3.78
Solvent content (%): 67.48
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: 2018-03-14
Crystal Structure of a threonine-selective RCR E3 ligase (PDB entry 5O6C)
Macromolecule: E3 ubiquitin-protein ligase MYCBP2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 263 residues
Sequence: SATSLKQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINHIVLKDLLDPIKELYEDVRRKALMRLEYEGLHKSEAITTPGVRFYNDPAGYAMNRYAYYVCYKCRKAYFGGEARCDAEAGRGDDYDPRELICGACSDVSRAQMCPKHGTDFLEYKCRYCCSVAVFFCFGTTHFCNACHDDFQRMTSIPKEELPHCPAGPKGKQLEGTECPLHVVHPPTGEEFALGCGVCRNAHTF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.17192
R free: 0.1957
Average B factor: 28.7
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.7
Crystallization temperature (K): 277
Crystal growth procedure: 23.3 mM Na2HPO4
23.3 mM (NH4)2SO4
23.3 mM NaNO3
18 % PEG500 MME
9 % PEG20000
Matthews coefficient: 3.38
Solvent content (%): 63.63
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2018-04-18
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM001763a (PDB entry 5RAV)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 372 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.179
R free: 0.2088
Average B factor: 32.492
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M bis-tris pH 5.5 21% PEG3350  0.3M magnesium chloride
Matthews coefficient: 2.8
Solvent content (%): 56
Ligand: cyclopropyl-[4-[(2~{S})-oxolan-2-yl]carbonylpiperazin-1-yl]methanone (S9G)
Ligand formula: C13 H20 N2 O3
Ligand molecular weight: 252.309
Ligand SMILES: C1CC(OC1)C(=O)N2CCN(CC2)C(=O)C3CC3
Ligand InChI: InChI=1S/C13H20N2O3/c16-12(10-3-4-10)14-5-7-15(8-6-14)13(17)11-2-1-9-18-11/h10-11H,1-9H2/t11-/m0/s1
Release date: 2020-04-22
SMYD2 in complex with AZ378 (PDB entry 5KJL)
Macromolecule: N-lysine methyltransferase SMYD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 429 residues
Sequence: GLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLEFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIESH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.172
R free: 0.236
Average B factor: 50.17
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 0.1 M Tris-HCl, 5% ethanol
Matthews coefficient: 3.21
Solvent content (%): 61.64
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: 2016-12-07
Human DNA polymerase beta pre-catalytic 8-oxoG:dA extension complex with dTTP bound in non-planar conformation (PDB entry 5VS1)
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): 2.5
R work: 0.2106
R free: 0.2721
Average B factor: 38.657
Crystallization method: VAPOR DIFFUSION, HANGING DROP
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: 2.26
Solvent content (%): 45.52
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2017-07-19
Crystal structure of CobB Ac3(A76G,Y92A, I131L, V187Y) in complex with H4K16-Acetyl peptide (PDB entry 6RXS)
Macromolecule: NAD-dependent protein deacylase
Type: Protein, polypeptide(L)
Source organism: Escherichia coli K-12
EC number: 3.5.1
Sequence length: 254 residues
Sequence: MGSSHHHHHHSQDPKPRVLVLTGAGISAESGIRTFRAADGLWEEHRVEDVGTPEGFDRDPELVQAFANARRRQLQQPEIQPNAAHLALAKLQDALGDRFLLVTQNLDNLHERAGNTNVIHMHGELLKVRCSQSGQVLDWTGDVTPEDKCHCCQFPAPLRPHYVWFGEMPLGMDEIYMALSMADIFIAIGTSGHVYPAAGFVHEAKLHGAHTVELNLEPSQVGNEFAEKYYGPASQVVPEFVEKLLKGLKAGSIA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.599
R work: 0.1791
R free: 0.2046
Average B factor: 26.3026
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350
Matthews coefficient: 2.26
Solvent content (%): 45.62
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: 2020-04-15
Titin I110-I111 FnIII tandem from the MIR region (I/A5-I/A6) (PDB entry 8BVO)
Macromolecule: Titin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 199 residues
Sequence: GAMEPSAPKELKFGDITKDSVHLTWEPPDDDGGSPLTGYVVEKREVSRKTWTKVMDFVTDLEFTVPDLVQGKEYLFRVCARNKCGPGEPAYVDEPVNMSTPATVPDPPENVKWRDRTANSIFLTWDPPKNDGGSRIKGYIVERCPRGSDKWVACGEPVAETKMEVTGLEEGKWYAYRVKALNRQGASKPSRPTEEIQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.2235
R free: 0.2872
Average B factor: 78.67
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 24% (w/v) PEG 1500, 20% (w/v) glycerol
Matthews coefficient: 2.5
Solvent content (%): 50.77
Release date: 2023-02-15
GTA mutant without mercury - E303D (PDB entry 5CMI)
Macromolecule: Histo-blood group ABO system transferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.40
Sequence length: 294 residues
Sequence: FMVSLPRMVYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVRAYKRWQDVSMRRMEMISDFCERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPGFYGSSREAFTYERRPQSQAYIPKDEGDFYYLGGFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDDSHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVPKNHQAVRNPE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1809
R free: 0.2332
Average B factor: 29.97
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 30-40 mg/ml protein, 1% PEG (w/v) 4000, 4.5% MPD (v/v), 0.1 M ammonium sulfate, 0.07 M NaCl, 0.05 M ADA buffer, pH 7.5, 5 mM MnCl2 against a reservoir containing 2.7% (w/v) PEG 4000, 7% (v/v) MPD, 0.32 M ammonium sulfate, 0.25 M NaCl, and 0.2 M ADA pH 7.5
Matthews coefficient: 2.24
Solvent content (%): 45.07
Release date: 2016-07-20
PKG II's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-pCPT-cGMP (PDB entry 5JIZ)
Macromolecule: cGMP-dependent protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.12
Sequence length: 152 residues
Sequence: GSTAQARDEQYRNFLRSVSLLKNLPEDKLTKIIDCLEVEYYDKGDYIIREGEEGSTFFILAKGKVKVTQSTEGHDQPQLIKTLQKGEYFGEKALISDDVRSANIIAEENDVACLVIDRETFNQTVGTFEELQKYLEGYVANLNRDDEKRHAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1795
R free: 0.1984
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM CaCl2, 100 mM NaOAc, 30% MPD, pH 4.6, at 4oC
Matthews coefficient: 1.99
Solvent content (%): 38.34
Ligand: 2-amino-8-[(4-chlorophenyl)sulfanyl]-9-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-3,9-dihydro-6H-purin-6-one (6FW)
Ligand formula: C16 H15 Cl N5 O7 P S
Ligand molecular weight: 487.811
Ligand SMILES: c1cc(ccc1Sc2nc3c(n2C4C(C5C(O4)COP(=O)(O5)O)O)NC(=NC3=O)N)Cl
Ligand InChI: InChI=1S/C16H15ClN5O7PS/c17-6-1-3-7(4-2-6)31-16-19-9-12(20-15(18)21-13(9)24)22(16)14-10(23)11-8(28-14)5-27-30(25,26)29-11/h1-4,8,10-11,14,23H,5H2,(H,25,26)(H3,18,20,21,24)/t8-,10-,11-,14-/m1/s1
Release date: 2017-05-03
CRYSTAL STRUCTURE OF KRAS-G12C IN COMPLEX WITH COMPOUND 23 (BI-0474) (PDB entry 8AFB)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.12
R work: 0.202
R free: 0.222
Average B factor: 14.73
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 10% PEG8000, 10% PEG1000
Matthews coefficient: 2.02
Solvent content (%): 39.08
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: 2022-11-09
Human ADAR2d E488Y mutant complexed with dsRNA containing an abasic site opposite the edited base (PDB entry 6D06)
Macromolecule: Double-stranded RNA-specific editase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4.37
Sequence length: 403 residues
Sequence: LHLDQTPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGYGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.19012
R free: 0.25518
Average B factor: 64.39
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M MES:NaOH pH 6.5, 14% PEG 20,000
Matthews coefficient: 2.6
Solvent content (%): 57.76
Ligand: INOSITOL HEXAKISPHOSPHATE (IHP)
Ligand formula: C6 H18 O24 P6
Ligand molecular weight: 660.035
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C6H18O24P6/c7-31(8,9)25-1-2(26-32(10,11)12)4(28-34(16,17)18)6(30-36(22,23)24)5(29-35(19,20)21)3(1)27-33(13,14)15/h1-6H,(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3-,4+,5-,6-
Release date: 2019-02-20
Crystal structure of chimeric carbonic anhydrase XII with 2,3,6-trifluoro-5-{[(1R,2S)-2-hydroxy-1,2-diphenylethyl]amino}-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide (PDB entry 6YH9)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFKVEFDDSQDKAVLKGGPLDGTYRLTQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDAGKASQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLNECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.166
R free: 0.2041
Average B factor: 21.023
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate
Matthews coefficient: 2.01
Solvent content (%): 38.93
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: 2021-04-07
ROS1 with AstraZeneca ligand 1 (PDB entry 7Z5W)
Macromolecule: Proto-oncogene tyrosine-protein kinase ROS
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSTQEEIENLPAFPREKLTLRLLLGSGAFGEVYEGTAVDILGVGSGEIKVAVKTLKKGSTDQEKIEFLKEAHLMSKFNHPNILKQLGVCLLNEPQYIILELMEGGDLLTYLRKARMATFYGPLLTLVDLVDLCVDISKGCVYLERMHFIHRDLAARNCLVSVKDYTSPRIVKIGDFGLARDIYKNDYYRKRGEGLLPVRWMAPESLMDGIFTTQSDVWSFGILIWEILTLGHQPYPAHSNLDVLNYVQTGGRLEPPRNCPDDLWNLMTQCWAQEPDQRPTFHRIQDQLQLFRNFFLNSIYKSRDEANNSGVINESFEGEDGDVICLNSDLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.254
R work: 0.2232
R free: 0.2755
Average B factor: 62.52
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.66
Crystallization temperature (K): 293.15
Crystal growth procedure: 11% peg3350, 200mM AmSO4, PCTP 100mM pH 6.66. Grown in 15well plate. Seeded with previous crystals. ATP/Mg 10mM
Ligand: ~{N}-[6-methyl-2-[(2~{S})-2-[3-(3-methylpyrazin-2-yl)-1,2-oxazol-5-yl]pyrrolidin-1-yl]pyrimidin-4-yl]-1,3-thiazol-2-amine (IDW)
Ligand formula: C20 H20 N8 O S
Ligand molecular weight: 420.491
Ligand SMILES: Cc1cc(nc(n1)N2CCCC2c3cc(no3)c4c(nccn4)C)Nc5nccs5
Ligand InChI: InChI=1S/C20H20N8OS/c1-12-10-17(26-20-23-7-9-30-20)25-19(24-12)28-8-3-4-15(28)16-11-14(27-29-16)18-13(2)21-5-6-22-18/h5-7,9-11,15H,3-4,8H2,1-2H3,(H,23,24,25,26)/t15-/m0/s1
Release date: 2022-08-17
P21-activated kinase 1 in complex with a 4-azaindole inhibitor (PDB entry 6B16)
Macromolecule: Serine/threonine-protein kinase PAK 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: GSDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKNNHGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.285
R work: 0.2015
R free: 0.2496
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 25% PEG 3500, 0.2M Ammonium Sulfate and 0.1M Tris pH 8
Matthews coefficient: 2.44
Solvent content (%): 49.58
Ligand: N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)-N~2~-[(1S)-1-(1H-pyrrolo[3,2-b]pyridin-5-yl)ethyl]pyrimidine-2,4-diamine (C7Y)
Ligand formula: C19 H20 N8
Ligand molecular weight: 360.416
Ligand SMILES: CC(c1ccc2c(n1)cc[nH]2)Nc3nccc(n3)Nc4cc([nH]n4)C5CC5
Ligand InChI: InChI=1S/C19H20N8/c1-11(13-4-5-14-15(23-13)6-8-20-14)22-19-21-9-7-17(25-19)24-18-10-16(26-27-18)12-2-3-12/h4-12,20H,2-3H2,1H3,(H3,21,22,24,25,26,27)/t11-/m0/s1
Release date: 2017-10-25
Crystal Structure of human ASH1L-MRG15 complex (PDB entry 6INE)
Macromolecule: Mortality factor 4-like protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 177 residues
Sequence: SSDPMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDNKEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYTPLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1931
R free: 0.2372
Average B factor: 47.0485
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris-HCl pH 8.5, 20 % PEG 6000, 0.2 M Trimethylamine-N-oxide
Matthews coefficient: 2.62
Solvent content (%): 53.12
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: 2019-03-20
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-768 (PDB entry 7ABD)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 364 residues
Sequence: GSHMIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.41
R work: 0.1728
R free: 0.2266
Average B factor: 47.651
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 3350, 30% Ethylene glycol, 0.1 M HEPES pH 7.5
Matthews coefficient: 2.63
Solvent content (%): 53.3
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: 2021-10-06
BACE-1 in complex with (7aR)-7a-(5-cyanothiophen-2-yl)-6-(5-fluoro-4-methyl-6-(methylthio)pyrimidin-2-yl)-3-methyl-4-oxooctahydro-2H-pyrrolo[3,4-d]pyrimidin-2-iminium (PDB entry 5HDZ)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 414 residues
Sequence: LRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.1942
R free: 0.2068
Average B factor: 19.9315
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 15% PEG 3350, 200mM Na/K tartrate, 100mM Hepes
Matthews coefficient: 2.97
Solvent content (%): 58.54
Ligand: 5-{(2E,4aR,7aR)-6-[5-fluoro-4-methyl-6-(methylsulfanyl)pyrimidin-2-yl]-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl}thiophene-2-carbonitrile (954)
Ligand formula: C18 H18 F N7 O S2
Ligand molecular weight: 431.51
Ligand SMILES: Cc1c(c(nc(n1)N2CC3C(=O)N(C(=N)NC3(C2)c4ccc(s4)C#N)C)SC)F
Ligand InChI: InChI=1S/C18H18FN7OS2/c1-9-13(19)14(28-3)23-17(22-9)26-7-11-15(27)25(2)16(21)24-18(11,8-26)12-5-4-10(6-20)29-12/h4-5,11H,7-8H2,1-3H3,(H2,21,24)/t11-,18-/m0/s1
Release date: 2016-03-16