satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of human RIPK3-MLKL complex (PDB entry 7MON)
Macromolecule: Mixed lineage kinase domain-like protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 287 residues
Sequence: GAMGSQEQIKEIKKEQLSGSPWILLRENEVSTLYKGEYHRAPVAIKVFKKLQAGSIAIVRQTFNKEIKTMKKFESPNILRIFGICIDETVTPPQFSIVMEYCELGTLRELLDREKDLTLGKRMVLVLGAARGLYRLHHSEAPELHGKIRSSNFLVTQGYQVKLAGFELRKTQTSMSLGTTREKTDRVKSTAYLSPQELEDVFYQYDVKSEIYSFGIVLWEIATGDIPFQGCNSEKIRKLVAVKRQQEPLGEDCPSELREIIDECRAHDPSVRPSVDEILKKLSTFSK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.2089
R free: 0.2601
Average B factor: 43.6036
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 281.15
Crystal growth procedure: 0.2 M ammonium acetate
30%w/v PEG 4000
0.1 M trisodium citrate-citric acid pH 5.5
Matthews coefficient: 2.07
Solvent content (%): 40.45
Ligand: N-[4-({2-[(cyclopropanecarbonyl)amino]pyridin-4-yl}oxy)-3-fluorophenyl]-1-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carboxamide (ZL1)
Ligand formula: C27 H20 F2 N4 O4
Ligand molecular weight: 502.469
Ligand SMILES: c1cc(ccc1N2C=CC=C(C2=O)C(=O)Nc3ccc(c(c3)F)Oc4ccnc(c4)NC(=O)C5CC5)F
Ligand InChI: InChI=1S/C27H20F2N4O4/c28-17-5-8-19(9-6-17)33-13-1-2-21(27(33)36)26(35)31-18-7-10-23(22(29)14-18)37-20-11-12-30-24(15-20)32-25(34)16-3-4-16/h1-2,5-16H,3-4H2,(H,31,35)(H,30,32,34)
Release date: 2021-11-17
Human DNA polymerase beta crosslinked complex, 30 s Ca to Mg exchange (PDB entry 7RBJ)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 341 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.1878
R free: 0.2289
Average B factor: 30.312
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Citrate pH 5.5, 18% PEG6000
Matthews coefficient: 2.24
Solvent content (%): 45.01
Ligand: 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol (QPJ)
Ligand formula: C5 H14 O10 P2
Ligand molecular weight: 296.106
Ligand SMILES: C(CO)C(C(COP(=O)(O)O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C5H14O10P2/c6-2-1-5(15-17(11,12)13)4(7)3-14-16(8,9)10/h4-7H,1-3H2,(H2,8,9,10)(H2,11,12,13)/t4-,5+/m1/s1
Release date: 2022-03-09
The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1 (PDB entry 7VDP)
Macromolecule: Cyclin-dependent-like kinase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 292 residues
Sequence: SQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKELKHKNIVRLHDVLHSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVLHRDLKPQNLLINRNGELKLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAKLYSTSIDMWSAGCIFAELANAGRPLFPGNDVDDQLKRIFRLLGTPTEEQWPSMTKLPDYKPYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEALQHPYFSDFCPP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.2009
R free: 0.2287
Average B factor: 63.908
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350
Matthews coefficient: 2.77
Solvent content (%): 55.66
Ligand: [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol (65L)
Ligand formula: C23 H23 F N6 O2
Ligand molecular weight: 434.466
Ligand SMILES: c1cc(c(cc1n2ccc(n2)CO)F)Nc3cc4c(ccc(n4)OC5CCNCC5)cn3
Ligand InChI: InChI=1S/C23H23FN6O2/c24-19-11-17(30-10-7-16(14-31)29-30)2-3-20(19)27-22-12-21-15(13-26-22)1-4-23(28-21)32-18-5-8-25-9-6-18/h1-4,7,10-13,18,25,31H,5-6,8-9,14H2,(H,26,27)
Release date: 2022-03-09
Crystal structure of EP3 receptor bound to misoprostol-FA (PDB entry 6M9T)
Macromolecule: Prostaglandin E2 receptor EP3 subtype, Endolysin chimera
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 537 residues
Sequence: VFADYKDDDDGAPKETRGYGGDAPFCTRLNHSYTGMWAPERSAEARGNLTRPPGSGEDCGSVSVAFPITMLLTGFVGNALAMLLVSRSYRRRESKRKKSFLLCIGWLALTDLVGQLLTTPVVIVVYLSKQRWEHIDPSGRLCTFFGLTMTVFGLSSLFIASAMAVERALAIRAPHWYASHMKTRATRAVLLGVWLAVLAFALLPVLGVGQYTVQWPGTWCFISTGRGGNGTSSSHNWGNLFFASAFAFLGLLALTVTFSCNLATIKALVSRGSNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDATVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYGSWGRITTETAIQLMAIMCVLSVCWSPLLIMMLKMIFNQTSVEHCKTHTEKQKECNFFLIAVRLASLNQILDPWVYLLLRKILGRPLEVLFQGPHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2
R free: 0.242
Average B factor: 128.85
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM sodium citrate, pH 3.8-4.2, 10-35 mM magnesium sulfate, 20-23% v/v PEG400, 2.5% Jeffamine M-600
Matthews coefficient: 2.66
Solvent content (%): 53.72
Ligand: (11alpha,12alpha,13E,16S)-11,16-dihydroxy-16-methyl-9-oxoprost-13-en-1-oic acid (J9P)
Ligand formula: C21 H36 O5
Ligand molecular weight: 368.508
Ligand SMILES: CCCCC(C)(CC=CC1C(CC(=O)C1CCCCCCC(=O)O)O)O
Ligand InChI: InChI=1S/C21H36O5/c1-3-4-13-21(2,26)14-9-11-17-16(18(22)15-19(17)23)10-7-5-6-8-12-20(24)25/h9,11,16-17,19,23,26H,3-8,10,12-15H2,1-2H3,(H,24,25)/b11-9+/t16-,17-,19-,21+/m1/s1
Release date: 2018-12-05
A natural inhibitor of DYRK1A for treatment of diabetes mellitus (PDB entry 6LN1)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 347 residues
Sequence: VYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKRFEYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.699
R work: 0.2123
R free: 0.2769
Average B factor: 65.7556
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Bis-Tris, 17% PEG 1500, 30% ethylene glycol
Matthews coefficient: 3.02
Solvent content (%): 59.21
Ligand: 1,3,5,8-tetrakis(oxidanyl)xanthen-9-one (EKU)
Ligand formula: C13 H8 O6
Ligand molecular weight: 260.199
Ligand SMILES: c1cc(c2c(c1O)C(=O)c3c(cc(cc3O2)O)O)O
Ligand InChI: InChI=1S/C13H8O6/c14-5-3-8(17)10-9(4-5)19-13-7(16)2-1-6(15)11(13)12(10)18/h1-4,14-17H
Release date: 2021-10-06
Complement factor B in complex with 5-Bromo-3-chloro-N-(4,5-dihydro-1H-imidazol-2-yl)-7-methyl-1H-indol-4-amine (PDB entry 6T8U)
Macromolecule: Complement factor B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.47
Sequence length: 291 residues
Sequence: SLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.84
R work: 0.1976
R free: 0.2389
Average B factor: 25.84
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 2.4M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6
Matthews coefficient: 2.78
Solvent content (%): 55.79
Ligand: 5-bromanyl-3-chloranyl-~{N}-(1~{H}-imidazol-2-yl)-7-methyl-1~{H}-indol-4-amine (MVZ)
Ligand formula: C12 H10 Br Cl N4
Ligand molecular weight: 325.592
Ligand SMILES: Cc1cc(c(c2c1[nH]cc2Cl)Nc3[nH]ccn3)Br
Ligand InChI: InChI=1S/C12H10BrClN4/c1-6-4-7(13)11(18-12-15-2-3-16-12)9-8(14)5-17-10(6)9/h2-5,17H,1H3,(H2,15,16,18)
Release date: 2020-03-04
Crystal structure of human carboxypeptidase O in complex with NvCI (PDB entry 5MRV)
Macromolecule: Carboxypeptidase O
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17
Sequence length: 355 residues
Sequence: EVQASWSHPQFEKGADDDDKVPDPKLYDRSLAQHRQEIVDKSVSPWSLETYSYNIYHPMGEIYEWMREISEKYKEVVTQHFLGVTYETHPIYYLKISQPSGNPKKIIWMDCGIHAREWIAPAFCQWFVKEILQNHKDNSRIRKLLRNLDFYVLPVLNIDGYIYTWTTDRLWRKSRSPHNNGTCFGTDLNRNFNASWCSIGASRNCQDQTFCGTGPVSEPETKAVASFIESKKDDILCFLTMHSYGQLILTPYGYTKNKSSNHPEMIQVGQKAANALKAKYGTNYRVGSSADILYASSGSSRDWARDIGIPFSYTFELRDSGTYGFVLPEAQIQPTCEETMEAVLSVLDDVYAKHW
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.854
R work: 0.1846
R free: 0.2082
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 291.15
Crystal growth procedure: Drops were prepared by mixing equal volumes of protein solution (CPO:NvCI molar ratio, 1:0.5) at 5 mg/ml (in 5 mM Tris-HCl pH 7.3, 100 mM NaCl, 1 mM B-mercaptoetanol) and reservoir solution containning HEPES pH 7.0, 200 mM ammonium choride and 20% PEG6000.
Matthews coefficient: 2.74
Solvent content (%): 55.08
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: 2018-01-17
Crystal structure of PTP1B D181A/Q262A/C215A phosphatase domain with TYK2 activation loop phosphopeptide (PDB entry 8EYC)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 299 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPAFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHASAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIATADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.99
R work: 0.2174
R free: 0.2543
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281.15
Crystal growth procedure: 14% PEG 8K, 0.20 M Magnesium Acetate, 0.1 M MES (pH 6.5)
Matthews coefficient: 2.71
Solvent content (%): 54.55
Release date: 2023-08-16
Crystal Structure of human phosphodiesterase 10 in complex with [2-methyl-6-[2-(1-methyl-4-phenylimidazol-2-yl)ethynyl]imidazo[1,2-b]pyridazin-3-yl]methanol (PDB entry 5SFF)
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): 2.16
R work: 0.1732
R free: 0.2267
Average B factor: 49.575
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: 2.61
Solvent content (%): 52.93
Ligand: {(4S)-2-methyl-6-[(1-methyl-4-phenyl-1H-imidazol-2-yl)ethynyl]imidazo[1,2-b]pyridazin-3-yl}methanol (IKH)
Ligand formula: C20 H17 N5 O
Ligand molecular weight: 343.382
Ligand SMILES: Cc1c(n2c(n1)ccc(n2)C#Cc3nc(cn3C)c4ccccc4)CO
Ligand InChI: InChI=1S/C20H17N5O/c1-14-18(13-26)25-20(21-14)11-9-16(23-25)8-10-19-22-17(12-24(19)2)15-6-4-3-5-7-15/h3-7,9,11-12,26H,13H2,1-2H3
Release date: 2022-10-12
Caspase-8 specific unnatural amino acid peptides (PDB entry 4PS0)
Macromolecule: Caspase-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.56
Sequence length: 285 residues
Sequence: MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETDSGVDDDMACHKIPVEADFLYAYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSFDATFHAKKQIPCIVSMLTKELYFYHQLHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.153
R free: 0.1792
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.15 M sodium citrate, pH 5.5, 14% PEG 6000, 0.3% sodium azide, 0.01 M DTT, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Matthews coefficient: 2.37
Solvent content (%): 48.02
Release date: 2015-01-21
Human Carbonic anhydrase II mutant T199V bound by 2-[(1S)-2,3-Dihydro-1H-inden-1-ylamino]-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide (PDB entry 6RMX)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTVPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1702
R free: 0.2127
Average B factor: 18.907
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
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: 2.09
Solvent content (%): 41.05
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: 2020-06-03
Human cyclin-dependent kinase 2 in complex with inhibitor HB-29260 (PDB entry 8OY2)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 300 residues
Sequence: GAMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.618
R work: 0.21971
R free: 0.28261
Average B factor: 50.555
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: MES pH7.0, PEG3350, ammonium acetate
Matthews coefficient: 2.11
Solvent content (%): 41.79
Ligand: (1S,2S,11aS)-1-methoxy-1,4,7,10-tetramethyl-2,9-bis(oxidanyl)-2,11a-dihydrobenzo[b][1,4]benzodioxepine-3,6-dione (W5W)
Ligand formula: C18 H20 O7
Ligand molecular weight: 348.347
Ligand SMILES: Cc1cc(c(c2c1C(=O)OC3=C(C(=O)C(C(C3O2)(C)OC)O)C)C)O
Ligand InChI: InChI=1S/C18H20O7/c1-7-6-10(19)8(2)13-11(7)17(22)25-14-9(3)12(20)15(21)18(4,23-5)16(14)24-13/h6,15-16,19,21H,1-5H3/t15-,16+,18+/m1/s1
Release date: 2023-11-29
Structure of human Senp7 with SUMO2 (PDB entry 7R2E)
Macromolecule: Sentrin-specific protease 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22
Sequence length: 345 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASTSNPDEEWREVRHTGLVQKLIVYPPPPTKGGLGVTNEDLECLEEGEFLNDVIIDFYLKYLILEKASDELVERSHIFSSFFYKCLTRKENNLTEDNPNLSMAQRRHKRVRTWTRHINIFNKDYIFVPVNESSHWYLAVICFPWLEEAVYEDFPQTVSQQSQAQQSQNDNKTIDNDLRTTSTLSLSAEDSQSTESNMSVPKKMCKRPCILILDSLKAASVQNTVQNLREYLEVEWEVKLKTHRQFSKTNMVDLCPKVPKQDNSSDCGVYLLQYVESFFKDPIVNFELPIHLEKWFPRHVIKTKREDIRELILKLHLQQQKGSSS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.1841
R free: 0.2304
Average B factor: 36.7846
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Sodium HEPES 7.0, 15 % w/v PEG 20,000
Matthews coefficient: 2.26
Solvent content (%): 45.59
Ligand: prop-2-en-1-amine (AYE)
Ligand formula: C3 H7 N
Ligand molecular weight: 57.094
Ligand SMILES: C=CCN
Ligand InChI: InChI=1S/C3H7N/c1-2-3-4/h2H,1,3-4H2
Release date: 2022-12-07
Crystal structure of Werner syndrome helicase complexed with AMP-PCP (PDB entry 8YLE)
Macromolecule: Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 430 residues
Sequence: NEGEEDDDKDFLWPAPNEEQVTCLKMYFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPACFLGSAQSENVLTDIKLGKYRIVYVTPEYCSGNMGLLQQLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTGNILQDLQPFLVKTSSHWEFEGPTIIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQVQKASLGIMGTEKCCDNCRSRLDHA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1833
R free: 0.2143
Average B factor: 30.67
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: pH 6.5,0.1 M Amino acids,0.1 M Buffer System 1, 30.00% % v/v EDO_P8K
Matthews coefficient: 2.4
Solvent content (%): 48.85
Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER (ACP)
Ligand formula: C11 H18 N5 O12 P3
Ligand molecular weight: 505.208
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
Release date: 2024-04-10
Crystal structure analysis of human CKB complex with a covalent compound (PDB entry 7TUN)
Macromolecule: Creatine kinase B-type
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.3.2
Sequence length: 401 residues
Sequence: MGSSHHHHHHSSGENLYFQGMPFSNSHNALKLRFPAEDEFPDLSAHNNHMAKVLTPELYAELRAKSTPSGFTLDDVIQTGVDNPGHPYIMTVGCVAGDEESYEVFKDLFDPIIEDRHGGYKPSDEHKTDLNPDNLQGGDDLDPNYVLSSRVRTGRSIRGFCLPPHCSRGERRAIEKLAVEALSSLDGDLAGRYYALKSMTEAEQQQLIDDHFLFDKPVSPLLLASGMARDWPDARGIWHNDNKTFLVWVNEEDHLRVISMQKGGNMKEVFTRFCTGLTQIETLFKSKDYEFMWNPHLGYILTCPSNLGTGLRAGVHIKLPNLGKHEKFSEVLKRLRLQKRGTGGVDTAAVGGVFDVSNADRLGFSEVELVQMVVDGVKLLIEMEQRLEQGQAIDDLMPAQK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.93
R work: 0.2047
R free: 0.2638
Average B factor: 80.7713
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.7M Ammonium citrate, pH 7.4
Matthews coefficient: 2.29
Solvent content (%): 46.32
Ligand: (2S)-4-(chloroacetyl)-3,4-dihydro-2H-1,4-benzoxazine-2-carboxamide (KLU)
Ligand formula: C11 H11 Cl N2 O3
Ligand molecular weight: 254.67
Ligand SMILES: c1ccc2c(c1)N(CC(O2)C(=O)N)C(=O)CCl
Ligand InChI: InChI=1S/C11H11ClN2O3/c12-5-10(15)14-6-9(11(13)16)17-8-4-2-1-3-7(8)14/h1-4,9H,5-6H2,(H2,13,16)/t9-/m0/s1
Release date: 2023-02-15
X-ray structure of human PPARalpha ligand binding domain-GW7647-SRC1 coactivator peptide co-crystals obtained by delipidation and co-crystallization (PDB entry 7BQ3)
Macromolecule: Peroxisome proliferator-activated receptor alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 273 residues
Sequence: GSHMTADLKSLAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYRDMY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1928
R free: 0.2371
Average B factor: 36.1825
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Tris (pH 8.5), 25%(w/v) PEG3350
Matthews coefficient: 2.31
Solvent content (%): 46.84
Ligand: 2-[(4-{2-[(4-cyclohexylbutyl)(cyclohexylcarbamoyl)amino]ethyl}phenyl)sulfanyl]-2-methylpropanoic acid (2VN)
Ligand formula: C29 H46 N2 O3 S
Ligand molecular weight: 502.752
Ligand SMILES: CC(C)(C(=O)O)Sc1ccc(cc1)CCN(CCCCC2CCCCC2)C(=O)NC3CCCCC3
Ligand InChI: InChI=1S/C29H46N2O3S/c1-29(2,27(32)33)35-26-18-16-24(17-19-26)20-22-31(28(34)30-25-14-7-4-8-15-25)21-10-9-13-23-11-5-3-6-12-23/h16-19,23,25H,3-15,20-22H2,1-2H3,(H,30,34)(H,32,33)
Release date: 2020-11-11
Discovery of Lu AF11167, a Phosphodiesterase 10A inhibitor clinical candidate (PDB entry 7QPM)
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: 340 residues
Sequence: MEKLSYHSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWRHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1741
R free: 0.24952
Average B factor: 38.644
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Hepes, 18% PEG3350
Matthews coefficient: 2.03
Solvent content (%): 39.29
Ligand: 5,7-dimethyl-2-[(1-methyl-4-phenyl-imidazol-2-yl)sulfanylmethyl]imidazo[1,2-a]pyrimidine (EEI)
Ligand formula: C19 H19 N5 S
Ligand molecular weight: 349.453
Ligand SMILES: Cc1cc(n2cc(nc2n1)CSc3nc(cn3C)c4ccccc4)C
Ligand InChI: InChI=1S/C19H19N5S/c1-13-9-14(2)24-10-16(21-18(24)20-13)12-25-19-22-17(11-23(19)3)15-7-5-4-6-8-15/h4-11H,12H2,1-3H3
Release date: 2023-04-19