satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of fragment 2-(Benzo[d]thiazol-2-yl)acetic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain (PDB entry 6CE8)
Macromolecule: Histone deacetylase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 107 residues
Sequence: GSPLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNKFGEDMPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1477
R free: 0.168
Average B factor: 12.856
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 291
Crystal growth procedure: 2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol
Matthews coefficient: 2.09
Solvent content (%): 41.07
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: 2018-02-28
Ternary DNA Polymerase Beta bound to DNA containing template FapydG incoming TTP analog (PDB entry 8VFD)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1997
R free: 0.2422
Average B factor: 33.12
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
Matthews coefficient: 2.35
Solvent content (%): 47.74
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2024-05-08
HIF prolyl hydroxylase 2 (PHD2-R281C/P317C) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-1) (PDB entry 5L9V)
Macromolecule: Hypoxia-inducible factor 1-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 19 residues
Sequence: DACTLLAPAAGDTIISLCF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.829
R work: 0.1694
R free: 0.1904
Average B factor: 40
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M ammonium chloride, 20 % w/v polyethylene glycol 3350
Matthews coefficient: 2.18
Solvent content (%): 43.6
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2016-08-31
Structure of Ack1 kinase in complex with a selective inhibitor (PDB entry 7KP6)
Macromolecule: Activated CDC42 kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 287 residues
Sequence: GAMGSGEGPLQSLTCLIGEKDLRLLEKLGDGSFGVVRRGEWDAPSGKTVSVAVKCLKPDVLSQPEAMDDFIREVNAMHSLDHRNLIRLYGVVLTPPMKMVTELAPLGSLLDRLRKHQGHFLLGTLSRYAVQVAEGMGYLESKRFIHRDLAARNLLLATRDLVKIGDFGLMRALPQNDDHYVMQEHRKVPFAWCAPESLKTRTFSHASDTWMFGVTLWEMFTYGQEPWIGLNGSQILHKIDKEGERLPRPEDCPQDIYNVMVQCWAHKPEDRPTFVALRDFLLEAQPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1779
R free: 0.2033
Average B factor: 32.4276
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 50mM Bis-Tris (pH 6.5), 23 % (w/v) polyethylene glycol 3350, 100 mM MgCl2, and 2.5% Glycerol
Matthews coefficient: 2.19
Solvent content (%): 43.76
Ligand: 5-chloro-N~2~-[4-(4-methylpiperazin-1-yl)phenyl]-N~4~-{[(2R)-oxolan-2-yl]methyl}pyrimidine-2,4-diamine (WTP)
Ligand formula: C20 H27 Cl N6 O
Ligand molecular weight: 402.921
Ligand SMILES: CN1CCN(CC1)c2ccc(cc2)Nc3ncc(c(n3)NCC4CCCO4)Cl
Ligand InChI: InChI=1S/C20H27ClN6O/c1-26-8-10-27(11-9-26)16-6-4-15(5-7-16)24-20-23-14-18(21)19(25-20)22-13-17-3-2-12-28-17/h4-7,14,17H,2-3,8-13H2,1H3,(H2,22,23,24,25)/t17-/m1/s1
Release date: 2022-02-09
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z30820160 (PDB entry 7FRK)
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): 1.8
R work: 0.1583
R free: 0.1892
Average B factor: 39.846
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Matthews coefficient: 3.3
Solvent content (%): 62.71
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: 2022-11-23
CDK2/cyclin A2 in complex with 3H-pyrazolo[4,3-f]quinoline-based derivative HSD1368 (PDB entry 7B7S)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 299 residues
Sequence: SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.54
R work: 0.246
R free: 0.2906
Average B factor: 37.521
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 80% Morpheus condition 35 containing: 10% w/v PEG 4,000, 20% v/v glycerol, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.1 M Tris/Bicine pH 8.5 and 20% of JCSG+ condition 59 containing: 14.4 % w/v PEG 8,000, 20% v/v Glycerol, 0.16 M calcium acetate, 0.08 M sodium cacodylate pH 6.5
Matthews coefficient: 3.19
Solvent content (%): 61.42
Ligand: 7-(3-(trifluoromethyl)-1H-pyrazol-4yl)-3,8,10,11-tetrahydropyrazolo[4,3-f]thiopyrano[3,4-c]quinoline 9-oxide (T1T)
Ligand formula: C17 H12 F3 N5 O S
Ligand molecular weight: 391.37
Ligand SMILES: c1cc2c(c3c1[nH]nc3)c4c(c(n2)c5cn[nH]c5C(F)(F)F)CS(=O)CC4
Ligand InChI: InChI=1S/C17H12F3N5OS/c18-17(19,20)16-10(6-22-25-16)15-11-7-27(26)4-3-8(11)14-9-5-21-24-12(9)1-2-13(14)23-15/h1-2,5-6H,3-4,7H2,(H,21,24)(H,22,25)/t27-/m1/s1
Release date: 2021-08-04
DNA Polymerase Lambda, TTP:At Mg2+ Product State Ternary Complex, 960 min (PDB entry 7M48)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 329 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.1839
R free: 0.2204
Average B factor: 42.2932
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.84
Solvent content (%): 56.63
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2022-07-06
Crystal structure of CK2 bound by compound 7 (PDB entry 7AY9)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 342 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.166
R free: 0.207
Average B factor: 35.66
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 22-26% PEG 6000 ( w/v ), 0.2 M ammonium sulfate and 0.1 M MES (pH 6.5).
Matthews coefficient: 3.09
Solvent content (%): 60.23
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: 2021-11-24
Crystal structure of HHD2 domain of hRTEL1 (PDB entry 8P8H)
Macromolecule: Regulator of telomere elongation helicase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 97 residues
Sequence: SMGKQGQHAVSAYLADARRALGSAGCSQLLAALTAYKQDDDLDKVLAVLAALTTAKPEDFPLLHRFSMFVRPHHKQRFSQTCTDLTGRPYPGMEPPG
Oligomeric state: Homo 7-mer
Stoichiometry: A7
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2142
R free: 0.257
Average B factor: 47.233
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M CHES pH 9.5, 30% PEG 3000
Matthews coefficient: 2.13
Solvent content (%): 42.24
Release date: 2024-06-12
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with FMOPL000609a (PDB entry 5QGT)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.189
R free: 0.2139
Average B factor: 42.198
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.36
Solvent content (%): 71.82
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2019-03-27
Crystal structure of human WDR5 in complex with PTEN (PDB entry 8X3S)
Macromolecule: WD repeat-containing protein 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 314 residues
Sequence: SSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.224
R free: 0.2586
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.2 M lithium sulfate monohydrate, 0.1 M HEPES at pH 7.5, 25% w/v polyethylene glycol 3350
Matthews coefficient: 1.81
Solvent content (%): 32.11
Release date: 2024-05-29
Crystal structure of NHL domain of TRIM2 (PDB entry 7B2R)
Macromolecule: Tripartite motif-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 277 residues
Sequence: SMNPIEDDLIFRVGTKGRNKGEFTNLQGVAASTNGKILIADSNNQCVQIFSNDGQFKSRFGIRGRSPGQLQRPTGVAVHPSGDIIIADYDNKWVSIFSSDGKFKTKIGSGKLMGPKGVSVDRNGHIIVVDNKACCVFIFQPNGKIVTRFGSRGNGDRQFAGPHFAAVNSNNEIIITDFHNHSVKVFNQEGEFMLKFGSNGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQVFDGSGSFLSYINTSADPLYGPQGLALTSDGHVVVADSGNHCFKVY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1558
R free: 0.1927
Average B factor: 22.533
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 25% Medium molecular weight PEG Smears, 0.1M MES pH 6.5
Matthews coefficient: 1.88
Solvent content (%): 34.47
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: 2021-01-13
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_XST00000280c (PDB entry 5QG0)
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): 1.753
R work: 0.1853
R free: 0.2089
Average B factor: 40.9598
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: 3.35
Solvent content (%): 63.3
Ligand: [2-(morpholin-4-yl)phenyl]methanol (JP4)
Ligand formula: C11 H15 N O2
Ligand molecular weight: 193.242
Ligand SMILES: c1ccc(c(c1)CO)N2CCOCC2
Ligand InChI: InChI=1S/C11H15NO2/c13-9-10-3-1-2-4-11(10)12-5-7-14-8-6-12/h1-4,13H,5-9H2
Release date: 2018-10-10
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with FMOPL000213a (PDB entry 5QOI)
Macromolecule: DCP2 (NUDT20)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.62
Sequence length: 167 residues
Sequence: SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLARLYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGFSSTGSTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.18
R free: 0.2367
Average B factor: 37.769
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M acetate, pH 4.5, 5-25% PEG3350
Matthews coefficient: 2.55
Solvent content (%): 51.72
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: 2019-05-08
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM001577a (PDB entry 5RAQ)
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): 1.85
R work: 0.1809
R free: 0.2162
Average B factor: 36.692
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: 2.77
Solvent content (%): 55.63
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2020-04-22
Factor XII Fibronectin type II (FXII FnII) domain (PDB entry 7PRJ)
Macromolecule: Coagulation factor XII
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.38
Sequence length: 71 residues
Sequence: IPPWEAPKEHKYKAEEHTVVLTVTGEPCHFPFQYHRQLYHKCTHKGRPGPQPWCATTPNFDQDQRWGYCLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1922
R free: 0.2385
Average B factor: 20.8
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 292.15
Crystal growth procedure: 0.01 M Zinc chloride, 0.1 M Sodium acetate pH 5.0, 20 % (w/v) PEG 6000
Matthews coefficient: 1.44
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2022-10-05
Crystal structure of human BRR2 in complex with T-1206548 (PDB entry 5URM)
Macromolecule: U5 small nuclear ribonucleoprotein 200 kDa helicase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 1738 residues
Sequence: GGSDLDQGGEALAPRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPALKPKPFGSEEQLLPVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRRLDLVHTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQLLKPTLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKESIEEPSAKINVLLQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNRGWAQLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVVKKIEKKNFPFERLYDLNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKVELTITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLITFFVPVFEPLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLDLQPLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSKCISIEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYENIPIRHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQLSAELQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWSKDSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEERNALLQLTDSQIADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQLEREEEVTGPVIAPLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATGAHNYTLYFMSDAYMGCDQEYKFSVDVKEA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2121
R free: 0.2598
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.25-1.5M sodium malonate, 100mM sodium citrate pH 5.0-5.3, 10mg/ml BRR2
Matthews coefficient: 3.32
Solvent content (%): 62.92
Ligand: 3-(5-{[(2R)-5-amino-2-cyclohexyl-7-oxo-2,3-dihydro-7H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-6-yl]methyl}furan-2-yl)benzoic acid (8LV)
Ligand formula: C23 H24 N4 O4 S
Ligand molecular weight: 452.526
Ligand SMILES: c1cc(cc(c1)C(=O)O)c2ccc(o2)CC3=C(N4C(=NC3=O)SC(N4)C5CCCCC5)N
Ligand InChI: InChI=1S/C23H24N4O4S/c24-19-17(12-16-9-10-18(31-16)14-7-4-8-15(11-14)22(29)30)20(28)25-23-27(19)26-21(32-23)13-5-2-1-3-6-13/h4,7-11,13,21,26H,1-3,5-6,12,24H2,(H,29,30)/t21-/m1/s1
Release date: 2017-07-19
Human Gcn5 bound to propionyl-CoA (PDB entry 5H84)
Macromolecule: Histone acetyltransferase KAT2A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 168 residues
Sequence: GSGIIEFHVIGNSLTPKANRRVLLWLVGLQNVFSHQLPRMPKEYIARLVFDPKHKTLALIKDGRVIGGICFRMFPTQGFTEIVFCAVTSNEQVKGYGTHLMNHLKEYHIKHNILYFLTYADEYAIGYFKKQGFSKDIKVPKSRYLGYIKDYEGATLMECELNPRIPYT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1637
R free: 0.19534
Average B factor: 19.664
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 20% (v/v) ethanol, 100 mM Tris, pH 9.0
Matthews coefficient: 2.02
Solvent content (%): 39.05
Ligand: propionyl Coenzyme A (1VU)
Ligand formula: C24 H40 N7 O17 P3 S
Ligand molecular weight: 823.597
Ligand SMILES: CCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C24H40N7O17P3S/c1-4-15(33)52-8-7-26-14(32)5-6-27-22(36)19(35)24(2,3)10-45-51(42,43)48-50(40,41)44-9-13-18(47-49(37,38)39)17(34)23(46-13)31-12-30-16-20(25)28-11-29-21(16)31/h11-13,17-19,23,34-35H,4-10H2,1-3H3,(H,26,32)(H,27,36)(H,40,41)(H,42,43)(H2,25,28,29)(H2,37,38,39)/t13-,17-,18-,19+,23-/m1/s1
Release date: 2016-03-23
Crystal structure of human carbonic anhydrase II in complex with the 4-(2-iso-propylphenyl)benzenesulfonamide inhibitor (PDB entry 5E2S)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 258 residues
Sequence: HHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1702
R free: 0.1963
Average B factor: 14.272
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, Tris 50 mM
Matthews coefficient: 2.09
Solvent content (%): 41.18
Ligand: 2'-(propan-2-yl)biphenyl-4-sulfonamide (5CX)
Ligand formula: C15 H17 N O2 S
Ligand molecular weight: 275.366
Ligand SMILES: CC(C)c1ccccc1c2ccc(cc2)S(=O)(=O)N
Ligand InChI: InChI=1S/C15H17NO2S/c1-11(2)14-5-3-4-6-15(14)12-7-9-13(10-8-12)19(16,17)18/h3-11H,1-2H3,(H2,16,17,18)
Release date: 2016-01-20