satarupa22/MacromolecularLigandDB huggingface dataset:
LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N44 i.e. 3-((2-(pyridin-2-yl)-6-(4-(vinylsulfonyl)-1,4-diazepan-1-yl)pyrimidin-4-yl)amino)propanoic acid (PDB entry 6DQ6)
Macromolecule: Linked KDM5A Jmj Domain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.587
R work: 0.1798
R free: 0.2023
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.25
Solvent content (%): 45.44
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: 2018-11-21
Crystal structure of human ACC2 BC domain in complex with ND-646, the primary amide of ND-630 (PDB entry 5KKN)
Macromolecule: Acetyl-CoA carboxylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.4.1.2
Sequence length: 540 residues
Sequence: MGSSHHHHHHENLYFQGLHRDFTVASPAEFVTRFGGDRVIEKVLIANNGIAAVKCMRSIRRWAYEMFRNERAIRFVVMVTPEDLKANAEYIKMADHYVPVPGGPNNNNYANVELIVDIAKRIPVQAVWAGWGHASENPKLPELLCKNGVAFLGPPSEAMWALGDKIASTVVAQTLQVPTLPWSGSGLTVEWTEDDLQQGKRISVPEDVYDKGCVKDVDEGLEAAERIGFPLMIKASEGGGGKGIRKAESAEDFPILFRQVQSEIPGSPIFLMKLAQHARHLEVQILADQYGNAVSLFGRDCSIQRRHQKIVEEAPATIAPLAIFEFMEQCAIRLAKTVGYVSAGTVEYLYSQDGSFHFLELNPRLQVEHPCTEMIADVNLPAAQLQIAMGVPLHRLKDIRLLYGESPWGVTPISFETPSNPPLARGHVIAARITSENPDEGFKPSSGTVQELNFRSSKNVWGYFSVAATGGLHEFADSQFGHCFSWGENREEAISNMVVALKELSIRGDFRTTVEYLINLLETESFQNNDIDTGWLDYLI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.21966
R free: 0.26563
Average B factor: 23.055
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris pH 7, 2.8 M sodium formate
Matthews coefficient: 3.41
Solvent content (%): 63.89
Ligand: 2-[1-[(2~{R})-2-(2-methoxyphenyl)-2-(oxan-4-yloxy)ethyl]-5-methyl-6-(1,3-oxazol-2-yl)-2,4-bis(oxidanylidene)thieno[2,3-d]pyrimidin-3-yl]-2-methyl-propanamide (6U3)
Ligand formula: C28 H32 N4 O7 S
Ligand molecular weight: 568.641
Ligand SMILES: Cc1c2c(sc1c3ncco3)N(C(=O)N(C2=O)C(C)(C)C(=O)N)CC(c4ccccc4OC)OC5CCOCC5
Ligand InChI: InChI=1S/C28H32N4O7S/c1-16-21-24(33)32(28(2,3)26(29)34)27(35)31(25(21)40-22(16)23-30-11-14-38-23)15-20(39-17-9-12-37-13-10-17)18-7-5-6-8-19(18)36-4/h5-8,11,14,17,20H,9-10,12-13,15H2,1-4H3,(H2,29,34)/t20-/m0/s1
Release date: 2016-07-13
Zinc finger region of human TET1 in complex with CpG DNA (PDB entry 6ASD)
Macromolecule: DNA (5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*TP*GP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 12 residues
Sequence: GCCACCGGTGGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.2016
R free: 0.235
Average B factor: 36.226
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 25% PEG-3350, 0.2 M ammonium acetate, 0.1 M HEPES
Matthews coefficient: 2.6
Solvent content (%): 52.2
Ligand: UNKNOWN ATOM OR ION (UNX)
Ligand formula: X
Ligand SMILES: *
Release date: 2017-10-18
HUMAN DNA POLYMERASE ETA INSERTION COMPLEX (PDB entry 8EVE)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1891
R free: 0.2443
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES PH 5.5, 5mM Calcium Chloride, 15-22% PEG 2000 MME
Matthews coefficient: 2.12
Solvent content (%): 41.9
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2023-08-02
Crystal structure of human PI3K-gamma in complex with benzimidazole inhibitor 5 (PDB entry 5EDS)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 959 residues
Sequence: SEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVTSKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDTPGAILQSFFTKMAKKKSLMDIPESQSEQDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRKEEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRNTDLTVFVEANIQHGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSSKASAESPSSESKGKVQLLYYVNLLLIDHRFLLRRGEYVLHMWQISGKGEDQGSFNADKLTSATNPDKENSMSISILLDNYCHPIALPKHQPTPDPEGDRVRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKHPKAYPKLFSSVKWGQQEIVAKTYQLLARREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIEMLQKVTLDIKSLSAEKYDVSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLNHWLKEKSPTEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKNEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLGIKQGEKHSA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2077
R free: 0.2733
Average B factor: 73.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 3350, 0.1 M Tris (pH 7.3), 0.25 M ammonium sulfate, 2 mM DTT
Matthews coefficient: 2.38
Solvent content (%): 48.35
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: 2015-12-30
Human DNA Pol eta S113A with dT-ended primer and dATP: in crystallo reaction for 480s (PDB entry 7M7U)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERAAIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.1789
R free: 0.2219
Average B factor: 27.6212
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: 15% PEG 2000 MME,
100 mM MES
Matthews coefficient: 2.08
Solvent content (%): 40.89
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: 2021-06-02
Crystal Structure of EGFR T790M/V948R in Complex with Covalent Pyrrolopyrimidine 18d (PDB entry 6TFW)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 333 residues
Sequence: GSHMASGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.2229
R free: 0.2447
Average B factor: 58.5162
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30 % PEG3350, 100 mM MgSO4, 4 % ethylen glycole 7.0 mg/mL EGFR T790M/V948R (in 100 mM NaCl, 25 mM Tris-HCl, 10 % glycerol, 1 mM TCEP, pH 8.0) 1 ul reservoir + 1 ul protein solution)
Matthews coefficient: 2.29
Solvent content (%): 46.19
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: 2020-09-30
Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing spiroiminodihydantoin (Sp) (PDB entry 6LWC)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 295 residues
Sequence: MGQGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGKGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.91
R work: 0.1906
R free: 0.2429
Average B factor: 115.328
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000
Matthews coefficient: 2.77
Solvent content (%): 55.59
Release date: 2021-06-09
Identification of a New Zinc Binding Chemotype by Fragment Screening (PDB entry 5U0E)
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): 1.27
R work: 0.12585
R free: 0.14751
Average B factor: 14.068
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3; concentrated CA II at ~10 mg mL-1 was set up with seeding; dry compound was added to crystals several days before harvesting and data collection
Matthews coefficient: 2.11
Solvent content (%): 41.58
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2017-08-30
Structure of DYRK1A in complex with compound 1 (PDB entry 7A4R)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 355 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1621
R free: 0.1937
Average B factor: 20.051
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES buffer at pH 6.5, 12% Peg3350, 0.2M MgCl2
Matthews coefficient: 2.3
Solvent content (%): 46.52
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: 2021-06-30
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000601a (PDB entry 5QE7)
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): 1.713
R work: 0.213
R free: 0.233
Average B factor: 42.1966
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: 3.32
Solvent content (%): 62.9
Ligand: 1-(3,4-dimethoxyphenyl)methanamine (JHD)
Ligand formula: C9 H13 N O2
Ligand molecular weight: 167.205
Ligand SMILES: COc1ccc(cc1OC)CN
Ligand InChI: InChI=1S/C9H13NO2/c1-11-8-4-3-7(6-10)5-9(8)12-2/h3-5H,6,10H2,1-2H3
Release date: 2018-10-10
Structure of CDC2-Like Kinase 2 (CLK2) in Complex with Compound T-025 [N2-methyl-N4-(pyrimidin-2-ylmethyl)-5-(quinolin-6-yl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine] (PDB entry 5UNP)
Macromolecule: Dual specificity protein kinase CLK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 369 residues
Sequence: GGSRSSSHSSRRAKSVEDDAEGHLIYHVGDWLQERYEIVSTLGEGTFGRVVQCVDHRRGGARVALKIIKNVEKYKEAARLEINVLEKINEKDPDNKNLCVQMFDWFDYHGHMCISFELLGLSTFDFLKDNNYLPYPIHQVRHMAFQLCQAVKFLHDNKLTHTDLKPENILFVNSDYELTYNLEKKRDERSVKSTAVRVVDFGSATFDHEHHSTIVSTRHYRAPEVILELGWSQPCDVWSIGCIIFEYYVGFTLFQTHDNREHLAMMERILGPIPSRMIRKTRKQKYFYRGRLDWDENTSAGRYVRENCKPLRRYLTSEAEEHHQLFDLIESMLEYEPAKRLTLGEALQHPFFARLRAEPPNKLWDSSRD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.92
R work: 0.20062
R free: 0.23385
Average B factor: 106.189
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Hepes (pH 7.0), 0.2M KBr, 0.2M KSCN, 0.4-1.8% PGA (poly-gama-glutamic acid) and 1-4% PEG MME M.W. 2,000
Matthews coefficient: 3.58
Solvent content (%): 65.6
Ligand: N~2~-methyl-N~4~-[(pyrimidin-2-yl)methyl]-5-(quinolin-6-yl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine (8FY)
Ligand formula: C21 H18 N8
Ligand molecular weight: 382.421
Ligand SMILES: CNc1nc2c(c(c[nH]2)c3ccc4c(c3)cccn4)c(n1)NCc5ncccn5
Ligand InChI: InChI=1S/C21H18N8/c1-22-21-28-19-18(20(29-21)27-12-17-24-8-3-9-25-17)15(11-26-19)13-5-6-16-14(10-13)4-2-7-23-16/h2-11H,12H2,1H3,(H3,22,26,27,28,29)
Release date: 2018-05-09
HDM2 in complex with compound 56 (PDB entry 7NA2)
Macromolecule: Isoform 11 of E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 110 residues
Sequence: GSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSDSGTSVSEN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.186
R free: 0.2585
Average B factor: 33.682
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: undisclosed
Matthews coefficient: 1.99
Solvent content (%): 38.27
Ligand: 3-[4-(5-chloropyridin-3-yl)-2-[(4aR,7aR)-hexahydrocyclopenta[b][1,4]oxazin-4(4aH)-yl]-3-{[(1r,4R)-4-methylcyclohexyl]methyl}-3H-imidazo[4,5-c]pyridin-6-yl]-1,2,4-oxadiazol-5(4H)-one (1I0)
Ligand formula: C28 H32 Cl N7 O3
Ligand molecular weight: 550.052
Ligand SMILES: CC1CCC(CC1)Cn2c3c(cc(nc3c4cc(cnc4)Cl)C5=NOC(=O)N5)nc2N6CCOC7C6CCC7
Ligand InChI: InChI=1S/C28H32ClN7O3/c1-16-5-7-17(8-6-16)15-36-25-20(32-27(36)35-9-10-38-23-4-2-3-22(23)35)12-21(26-33-28(37)39-34-26)31-24(25)18-11-19(29)14-30-13-18/h11-14,16-17,22-23H,2-10,15H2,1H3,(H,33,34,37)/t16-,17-,22-,23-/m1/s1
Release date: 2021-11-10
Crystal structure of 1-hydroxy-3-(trifluoromethyl)pyridine-2(1H)-thione bound to human carbonic anhydrase II (PDB entry 4Q83)
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): 1.55
R work: 0.16937
R free: 0.19922
Average B factor: 10.337
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium Sulfate, pH 8.0, VAPOR DIFFUSION, temperature 291K
Matthews coefficient: 2.1
Solvent content (%): 41.49
Ligand: MERCURIBENZOIC ACID (MBO)
Ligand formula: C7 H5 Hg O2
Ligand molecular weight: 321.703
Ligand SMILES: c1cc(ccc1C(=O)O)[Hg]
Ligand InChI: InChI=1S/C7H5O2.Hg/c8-7(9)6-4-2-1-3-5-6;/h2-5H,(H,8,9);
Release date: 2015-03-11
Human jak1 kinase domain in complex with compound 7 (PDB entry 6ELR)
Macromolecule: Tyrosine-Protein Kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 301 residues
Sequence: DIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.181
R free: 0.205
Average B factor: 34.81
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 282
Crystal growth procedure: 2mM ligand, 27% (m/v) PEG6000, 0.1 M MES/NaOH pH 6.0, 5 mM DTT
Matthews coefficient: 2.53
Solvent content (%): 51.33
Ligand: [3-[[5-methyl-2-[[3-(4-methylpiperazin-1-yl)-5-methylsulfonyl-phenyl]amino]pyrimidin-4-yl]amino]phenyl]methanol (BFK)
Ligand formula: C24 H30 N6 O3 S
Ligand molecular weight: 482.598
Ligand SMILES: Cc1cnc(nc1Nc2cccc(c2)CO)Nc3cc(cc(c3)S(=O)(=O)C)N4CCN(CC4)C
Ligand InChI: InChI=1S/C24H30N6O3S/c1-17-15-25-24(28-23(17)26-19-6-4-5-18(11-19)16-31)27-20-12-21(14-22(13-20)34(3,32)33)30-9-7-29(2)8-10-30/h4-6,11-15,31H,7-10,16H2,1-3H3,(H2,25,26,27,28)
Release date: 2018-10-10
Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 4-10 (PDB entry 5AM8)
Macromolecule: ANGIOTENSIN-CONVERTING ENZYME
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1
Sequence length: 629 residues
Sequence: LDPGLQPGQFSADEAGAQLFAQSYQSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQQFTDPQLRRIIGAVRTLGSANLPLAKRQQYNALLSQMSRIYSTAKVCLPNKTATCWSLDPDLTNILASSRSYAMLLFAWEGWHNAAGIPLKPLYEDFTALSNEAYKQDGFTDTGAYWRSWYNSPTFEDDLEHLYQQLEPLYLNLHAFVRRALHRRYGDRYINLRGPIPAHLLGDMWAQSWENIYDMVVPFPDKPNLDVTSTMLQQGWQATHMFRVAEEFFTSLELSPMPPEFWEGSMLEKPADGREVVCHASAWDFYNRKDFRIKQCTRVTMDQLSTVHHEMGHIQYYLQYKDLPVSLRRGANPGFHEAIGDVLALSVSTPEHLHKIGLLDRVTNDTESDINYLLKMALEKIAFLPFGYLVDQWRWGVFSGRTPPSRYNFDWWYLRTKYQGICPPVTRNETHFDAGAKFHVPNVTPYIRYFVSFVLQFQFHEALCKEAGYEGPLHQCDIYRSTKAGAKLRKVLRAGSSRPWQEVLKDMVGLDALDAQPLLKYFQLVTQWLQEQNQQNGEVLGWPEYQWHPPLPDNYPEGIDLVTDEAEASKFVEEYDL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.18543
R free: 0.22382
Average B factor: 25.005
Crystallization pH: 8.5
Crystal growth procedure: 0.06 M DIVALENT CATIONS, 0.1 M TRIS/BICINE PH 8.5, 30 % PEG550MME/PEG20000
Matthews coefficient: 2.95
Solvent content (%): 58
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: 2016-01-13
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with myo-5-IP7, produced upon myo-IP6 phosphorylation by TvI (PDB entry 8TF9)
Macromolecule: Diphosphoinositol polyphosphate phosphohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.52
Sequence length: 148 residues
Sequence: MMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.16142
R free: 0.18782
Average B factor: 22.894
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 297
Crystal growth procedure: 10% w/v PEG8000, 10% v/v isopropanol, 200 mM lithium sulfate, 100 mM sodium acetate, pH 5.0, 5 mM IP6, soaked in 200 mM lithium chloride, 20% w/v PEG8000, 20% v/v isopropanol, 100 mM sodium acetate, pH 5.0, 20 mM magnesium chloride, 100 mM sodium fluoride in presence of TvIPK reaction solution with myo-IP6
Matthews coefficient: 2.46
Solvent content (%): 49.91
Ligand: (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate (I7P)
Ligand formula: C6 H19 O27 P7
Ligand molecular weight: 740.015
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C6H19O27P7/c7-34(8,9)27-1-2(28-35(10,11)12)4(30-37(16,17)18)6(32-40(25,26)33-39(22,23)24)5(31-38(19,20)21)3(1)29-36(13,14)15/h1-6H,(H,25,26)(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: 2023-11-15
apo-Carbonic Anhydrase II soaked in 3NPA before UV at 90 K (PDB entry 7Y2J)
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): 1.25
R work: 0.12185
R free: 0.16734
Average B factor: 14.455
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.07
Solvent content (%): 40.71
Release date: 2023-12-20