satarupa22/MacromolecularLigandDB huggingface dataset:
Pre-catalytic ternary complex of human Polymerase Mu with incoming nonhydrolyzable UMPNPP (PDB entry 5TWP)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 354 residues
Sequence: GSAAASPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.001
R work: 0.1852
R free: 0.2379
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 294
Crystal growth procedure: 95mM HEPES pH 7.5, 19% PEG4K
Matthews coefficient: 2.52
Solvent content (%): 51.2
Ligand: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine (2KH)
Ligand formula: C9 H16 N3 O14 P3
Ligand molecular weight: 483.156
Ligand SMILES: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C9H16N3O14P3/c13-5-1-2-12(9(16)10-5)8-7(15)6(14)4(25-8)3-24-27(17,18)11-28(19,20)26-29(21,22)23/h1-2,4,6-8,14-15H,3H2,(H,10,13,16)(H2,21,22,23)(H3,11,17,18,19,20)/t4-,6-,7-,8-/m1/s1
Release date: 2017-07-05
THE KINASE DOMAIN OF HUMAN SPLEEN TYROSINE (SYK) IN COMPLEX WITH GTC000226 (PDB entry 4YJS)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 281 residues
Sequence: PEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.1696
R free: 0.2257
Average B factor: 49.491
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 293
Crystal growth procedure: 32.5% Jeffamine ED-2001, 10% Glycerol, 0.1M MES pH6.8, 5mM DTT
Matthews coefficient: 1.95
Solvent content (%): 36.8
Ligand: 3-[{2-[(1,1-dioxido-2,3-dihydro-1,2-benzothiazol-6-yl)amino]pyrimidin-4-yl}(1H-indazol-4-yl)amino]propan-1-ol (4DN)
Ligand formula: C21 H21 N7 O3 S
Ligand molecular weight: 451.502
Ligand SMILES: c1cc2c(cn[nH]2)c(c1)N(CCCO)c3ccnc(n3)Nc4ccc5c(c4)S(=O)(=O)NC5
Ligand InChI: InChI=1S/C21H21N7O3S/c29-10-2-9-28(18-4-1-3-17-16(18)13-23-27-17)20-7-8-22-21(26-20)25-15-6-5-14-12-24-32(30,31)19(14)11-15/h1,3-8,11,13,24,29H,2,9-10,12H2,(H,23,27)(H,22,25,26)
Release date: 2015-09-30
Crystal structure of human tankyrase 2 in complex with 5-amino-3- phenyl-1,2-dihydroisoquinolin-1-one (PDB entry 4UVZ)
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): 1.6
R work: 0.16365
R free: 0.18851
Average B factor: 16.018
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M LISO4, 0.1 M TRIS HCL, 22% PEG3350, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
Matthews coefficient: 2.4
Solvent content (%): 49
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: 2015-07-29
Crystal structure of the human dual specificity 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the designed AR protein mbp3_16 (PDB entry 6D66)
Macromolecule: Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Escherichia coli K-12
EC number: 3.1.3.16
Sequence length: 520 residues
Sequence: MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAGGPVEILPFLYLGSAYHASRKDMLDALGITALINVSANCPNHFEGHYQYKSIPVEDNHKADISSWFNEAIDFIDSIKNAGGRVFVHSQAGISRSATICLAYLMRTNRVKLDEAFEFVKQRRSIISPNFSFMGQLLQFESQVLAHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.226
R work: 0.1594
R free: 0.2018
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.2 M DL-glutamic acid
0.2 M DL-alanine
0.2 M -glycine
0.2 M-DL-lysine
0.2 M DL-serine
0.1 M Tris: Bicine 
25% MPD
25% PEG1000
25% PEG3350
Matthews coefficient: 2.96
Solvent content (%): 58.38
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: 2018-09-19
Human Cytochrome P450 (CYP) 3A5 ternary complex with azamulin (PDB entry 7SV2)
Macromolecule: Cytochrome P450 3A5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.1
Sequence length: 480 residues
Sequence: MALYGTRTHGLFKRLGIPGPTPLPLLGNVLSYRQGLWKFDTECYKKYGKMWGTYEGQLPVLAITDPDVIRTVLVKECYSVFTNRRSLGPVGFMKSAISLAEDEEWKRIRSLLSPTFTSGKLKEMFPIIAQYGDVLVRNLRREAEKGKPVTLKDIFGAYSMDVITGTSFGVNIDSLNNPQDPFVESTKKFLKFGFLDPLFLSIILFPFLTPVFEALNVSLFPKDTINFLSKSVNRMKKSRLNDKQKHRLDFLQLMIDSQNSKETESHKALSDLELAAQSIIFIFAGYETTSSVLSFTLYELATHPDVQQKLQKEIDAVLPNKAPPTYDAVVQMEYLDMVVNETLRLFPVAIRLERTCKKDVEINGVFIPKGSMVVIPTYALHHDPKYWTEPEEFRPERFSKKKDSIDPYIYTPFGTGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLDTQGLLQPEKPIVLKVDSRDGHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.46
R work: 0.1877
R free: 0.2233
Average B factor: 63.54
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 297
Crystal growth procedure: Na Malonate, pH 6.5, 30% PEG 3350, n-decyl-beta-D-maltoside
Matthews coefficient: 2.21
Solvent content (%): 44.26
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2022-05-18
PTP1BC215S bound to Nephrin peptide substrate (PDB entry 4ZRT)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 298 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHSSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHED
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.16835
R free: 0.20743
Average B factor: 24.687
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 14.4% PEG 8000, 0.1 M HEPES (pH 7.5), 0.2 M MgCl2
Matthews coefficient: 2.68
Solvent content (%): 54.03
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2015-06-24
MEKK1 TOG domain (548-867) (PDB entry 6WHB)
Macromolecule: Mitogen-activated protein kinase kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 350 residues
Sequence: GPGTHYGTQQIPPAYKDLAEPWIQVFGMELVGCLFSRNWNVREMALRRLSHDVSGALLLANGESTGNSGGSSGSSPSGGATSGSSQTSISGDVVEACCSVLSMVCADPVYKVYVAALKTLRAMLVYTPCHSLAERIKLQRLLQPVVDTILVKCADANSRTSQLSISTLLELCKGQAGELAVGREILKAGSIGIGGVDYVLNCILGNQTESNNWQELLGRLCLIDRLLLEFPAEFYPHIVSTDVSQAEPVEIRYKKLLSLLTFALQSIDNSHSMVGKLSRRIYLSSARMVTTVPHVFSKLLEMLSVSSSTHFTRMRRRLMAIADEVEIAEAIQLGVEDTLDGQQDSFLQAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.90032055102
R work: 0.2070807354
R free: 0.229687564641
Average B factor: 61.378466522
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 290.15
Crystal growth procedure: 0.1 M Bis-Tris Propane pH 6.9, 1.5 M sodium acetate
Matthews coefficient: 2.15
Solvent content (%): 42.8
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2020-08-26
A Carbonic Anhydrase IX Mimic in Complex with a Saccharin-Based Inhibitor (PDB entry 4RIU)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.651
R work: 0.1514
R free: 0.1761
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6 M Sodium Citrate, 50mM Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Matthews coefficient: 2.07
Solvent content (%): 40.5
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: 2015-02-04
Crystal structure of HLA-B*07:02 with wild-type IDH2 peptide (PDB entry 6UJ8)
Macromolecule: HLA class I histocompatibility antigen, B-7 alpha chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 298 residues
Sequence: MGSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYWDRNTQIYKAQAQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHDQYAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGECVEWLRRYLENGKDKLERADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSSQSGSLHHILDAQKMVWNHR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.2156
R free: 0.2599
Average B factor: 42.004
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M MES pH 6.5, 0.2 M KI, 30% PEG4000
Matthews coefficient: 2.03
Solvent content (%): 39.48
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: 2021-05-05
Crystal Structure of human phosphodiesterase 10 in complex with 3-[2-(2,5-difluorophenyl)pyrazol-3-yl]-1-(3-methylsulfonylphenyl)pyridazin-4-one (PDB entry 5SIF)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1817
R free: 0.2309
Average B factor: 37.861
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.62
Solvent content (%): 53.06
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: 2022-10-12
Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (RB2L) (PDB entry 5C1D)
Macromolecule: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.255
Sequence length: 723 residues
Sequence: GPGSCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNGIDLKAFLDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIKPVE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.19461
R free: 0.22864
Average B factor: 45.3
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 294.15
Crystal growth procedure: 1.45 M Potassium diohydrogen phosphate, 8 mM EDTA, 1% xylitol (reservoir). 1.45 M Potassium diohydrogen phosphate, 8 mM EDTA, 1% xylitol, 0.5 M Ammonium sulfate (drop)
Matthews coefficient: 3.22
Solvent content (%): 61.84
Ligand: (2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (12V)
Ligand formula: C17 H27 N3 O16 P2 S
Ligand molecular weight: 623.419
Ligand SMILES: CC(=O)NC1C(C(C(SC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
Ligand InChI: InChI=1S/C17H27N3O16P2S/c1-6(22)18-10-13(26)12(25)8(4-21)39-16(10)35-38(31,32)36-37(29,30)33-5-7-11(24)14(27)15(34-7)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10-,11-,12-,13-,14-,15-,16+/m1/s1
Release date: 2015-08-05
Crystal structure of GSK-3b in complex with the imidazo[1,5-a]pyridine-3-carboxamide inhibitor 16 (PDB entry 6Y9S)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 350 residues
Sequence: SKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.2025
R free: 0.2493
Average B factor: 41.632
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.10 M TrisAc pH8.25
26 % PEG 8K
0.13 M NaCl
Matthews coefficient: 2.7
Solvent content (%): 54.46
Ligand: ~{N}-(oxan-4-ylmethyl)-6-(5-propan-2-yloxypyridin-3-yl)imidazo[1,5-a]pyridine-3-carboxamide (OHK)
Ligand formula: C22 H26 N4 O3
Ligand molecular weight: 394.467
Ligand SMILES: CC(C)Oc1cc(cnc1)c2ccc3cnc(n3c2)C(=O)NCC4CCOCC4
Ligand InChI: InChI=1S/C22H26N4O3/c1-15(2)29-20-9-18(11-23-13-20)17-3-4-19-12-24-21(26(19)14-17)22(27)25-10-16-5-7-28-8-6-16/h3-4,9,11-16H,5-8,10H2,1-2H3,(H,25,27)
Release date: 2020-05-20
The FK1 domain of FKBP51 in complex with SAFit-analog 23d (PDB entry 9EUA)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2562
R free: 0.3042
Average B factor: 45.416
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG3350, 0.2M ammonium thiocyanate, 0.1M HEPES-NaOH pH 7.5 10% ethylene glycol
Matthews coefficient: 2.42
Solvent content (%): 49.17
Ligand: (1-propylpyrazol-4-yl)methyl (2S)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate (A1H7D)
Ligand formula: C30 H43 N3 O6
Ligand molecular weight: 541.679
Ligand SMILES: CCCn1cc(cn1)COC(=O)C2CCCCN2C(=O)C(c3cc(c(c(c3)OC)OC)OC)C4CCCCC4
Ligand InChI: InChI=1S/C30H43N3O6/c1-5-14-32-19-21(18-31-32)20-39-30(35)24-13-9-10-15-33(24)29(34)27(22-11-7-6-8-12-22)23-16-25(36-2)28(38-4)26(17-23)37-3/h16-19,22,24,27H,5-15,20H2,1-4H3/t24-,27-/m0/s1
Release date: 2024-06-12
Crystal structure of human carbonic anhydrase II in complex with the 6-hydroxy-chromene-2-thione inhibitor (PDB entry 4WL4)
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): 1.1
R work: 0.109
R free: 0.1299
Average B factor: 15.743
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.6 M sodium citrate, Tris 50 mM
Matthews coefficient: 2.09
Solvent content (%): 41.18
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: 2015-10-14
Human Carbonic Anhydrase II bound N-(2-(2-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)ethoxy)ethyl)-4-sulfamoylbenzamide (PDB entry 8EXG)
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): 1.99
R work: 0.1872
R free: 0.2233
Average B factor: 20.67
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.6-3.0 M Ammonium sulfate in 50 mM Tris-Sulfate (pH 8)
Matthews coefficient: 2.09
Solvent content (%): 41.23
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2023-02-22
Crystal structure of DUSP22 mutant_N128A (PDB entry 7C8S)
Macromolecule: Dual specificity protein phosphatase 22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 157 residues
Sequence: GPMGNGMNKILPGLYIGNFKDARDAEQLSKNKVTHILSVHDSARPMLEGVKYLCIPAADSPSQNLTRHFKESIKFIHECRLRGESCLVHCLAGVSRSVTLVIAYIMTVTDFGWEDALHTVRAGRSCANPAVGFQRQLQEFEKHEVHQYRQWLKEEYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.31
R work: 0.1874
R free: 0.1965
Average B factor: 19.79
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, 30% PEG 3,350, 0.2 M Li2SO4
Matthews coefficient: 2.55
Solvent content (%): 51.76
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: 2020-10-28
Native state mass spectrometry, surface plasmon resonance and X-ray crystallography correlate strongly as a fragment screening combination (PDB entry 5FLQ)
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): 1.7
R work: 0.15455
R free: 0.21511
Average B factor: 15.597
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystal growth procedure: 15 MG/ML PROTEIN WITH 2.7 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5 AT 8 C IN SITTING DROPS.
Matthews coefficient: 2.1
Solvent content (%): 42.1
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2016-03-02
Crystal structure of the full-length human mitochondrial CCA-adding enzyme (PDB entry 4X4W)
Macromolecule: CCA tRNA nucleotidyltransferase 1, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.72
Sequence length: 416 residues
Sequence: MFTMKLQSPEFQSLFTEGLKSLTELFVKENHELRIAGGAVRDLLNGVKPQDIDFATTATPTQMKEMFQSAGIRMINNRGEKHGTITARLHEENFEITTLRIDVTTDGRHAEVEFTTDWQKDAERRDLTINSMFLGFDGTLFDYFNGYEDLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIVDKPGDHDPETLEAIAENAKGLAGISGERIWVELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPVTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLIKATDSSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSIPPFPVSGHDIRKVGISSGKEIGALLQQLREQWKKSGYQMEKDELLSYIKKTLEHHHHHH
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1539
R free: 0.1958
Average B factor: 32.81
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 290
Crystal growth procedure: 2.2M Ammonium Sulfate, 0.05M Na Citrate pH 5.5
Matthews coefficient: 3.05
Solvent content (%): 59.72
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: 2015-02-11