satarupa22/MacromolecularLigandDB huggingface dataset:
The PDZ domain of SNTG2 complexed with the phosphorylated PDZ-binding motif of RSK1 (PDB entry 7QQL)
Macromolecule: Gamma-2-syntrophin,Annexin A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 408 residues
Sequence: GSHMGNRRTVTLRRQPVGGLGLSIKGGSEHNVPVVISKIFEDQAADQTGMLFVGDAVLQVNGIHVENATHEEVVHLLRNAGDEVTITVEYLREAPGSAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.44
R work: 0.1953
R free: 0.2295
Average B factor: 66.7492
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Succinic acid pH 7.0 15% w/v PEG 3350
Matthews coefficient: 2.81
Solvent content (%): 56.17
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: 2022-04-20
The Fk1 domain of FKBP51 in complex with (2R,5S,12S)-12-(thiophen-2-yl)-2-[2-(3,4-dimethoxyphenyl)ethyl]-15,15-dimethyl-3,19-dioxa-10,13,16-triazatricyclo[18.3.1.0^5,^10]tetracosa-1(24),20,22-triene-4,11,14,17-tetrone (PDB entry 8CCG)
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): 1.3
R work: 0.1665
R free: 0.1998
Average B factor: 19.858
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 32% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate
Matthews coefficient: 2.4
Solvent content (%): 48.81
Ligand: (2~{R},5~{S},12~{S})-2-[2-(3,4-dimethoxyphenyl)ethyl]-15,15-dimethyl-12-thiophen-2-yl-3,19-dioxa-10,13,16-triazatricyclo[18.3.1.0^{5,10}]tetracosa-1(24),20,22-triene-4,11,14,17-tetrone (UBK)
Ligand formula: C35 H41 N3 O8 S
Ligand molecular weight: 663.78
Ligand SMILES: CC1(C(=O)NC(C(=O)N2CCCCC2C(=O)OC(c3cccc(c3)OCC(=O)N1)CCc4ccc(c(c4)OC)OC)c5cccs5)C
Ligand InChI: InChI=1S/C35H41N3O8S/c1-35(2)34(42)36-31(29-12-8-18-47-29)32(40)38-17-6-5-11-25(38)33(41)46-26(15-13-22-14-16-27(43-3)28(19-22)44-4)23-9-7-10-24(20-23)45-21-30(39)37-35/h7-10,12,14,16,18-20,25-26,31H,5-6,11,13,15,17,21H2,1-4H3,(H,36,42)(H,37,39)/t25-,26+,31+/m0/s1
Release date: 2023-04-26
X-ray crystal structure of chemically synthesized human lysozyme (PDB entry 6LFH)
Macromolecule: Lysozyme C
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 130 residues
Sequence: KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.1617
R free: 0.1957
Average B factor: 19.1047
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 298
Crystal growth procedure: Lysozyme sample (14 mg/mL) in 2.5 mM HEPES, 0.12 M lithium chloride mixed with reservoir solution containing 30 mM sodium phosphate, 2.5 M sodium chloride
Matthews coefficient: 1.93
Solvent content (%): 36.35
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: 2020-07-08
Notum-Fragment 199 (PDB entry 7B8O)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.2101
R free: 0.2335
Average B factor: 24.4347
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.99
Solvent content (%): 38.12
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: 2022-01-12
Crystal structure of human carbonic anhydrase II with 4-((2-hydroxy-3-(phenylselanyl)propyl)thio)benzenesulfonamide (PDB entry 7OK8)
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): 1.43
R work: 0.1417
R free: 0.1651
Average B factor: 13.047
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Matthews coefficient: 2.11
Solvent content (%): 41.57
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: 2022-06-01
Human protein kinase CK2 alpha in complex with coumestrol (PDB entry 6HNW)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 336 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1884
R free: 0.2246
Average B factor: 30.7231
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 32% PEG4000, 0.2 M Lithium Sulfate
Matthews coefficient: 1.98
Solvent content (%): 37.76
Ligand: Coumestrol (CUE)
Ligand formula: C15 H8 O5
Ligand molecular weight: 268.221
Ligand SMILES: c1cc2c(cc1O)oc-3c2C(=O)Oc4c3ccc(c4)O
Ligand InChI: InChI=1S/C15H8O5/c16-7-1-3-9-11(5-7)19-14-10-4-2-8(17)6-12(10)20-15(18)13(9)14/h1-6,16-17H
Release date: 2019-08-07
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000555a (PDB entry 7FQS)
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): 2.12
R work: 0.1652
R free: 0.2209
Average B factor: 46.993
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 (%): 62.73
Ligand: (2R,5R,6S)-2,3,4,5,6,7-hexahydro-1H-2,6-methanoazocino[5,4-b]indol-5-ol (JPV)
Ligand formula: C14 H16 N2 O
Ligand molecular weight: 228.29
Ligand SMILES: c1ccc2c(c1)c3c([nH]2)C4CC(C3)NCC4O
Ligand InChI: InChI=1S/C14H16N2O/c17-13-7-15-8-5-10-9-3-1-2-4-12(9)16-14(10)11(13)6-8/h1-4,8,11,13,15-17H,5-7H2/t8-,11+,13-/m0/s1
Release date: 2022-11-23
EGFR kinase domain mutant "TMLR" with compound 27 (PDB entry 5CAN)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.1961
R free: 0.2317
Average B factor: 69.8
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: PEG 10000, ethylene glycol
Matthews coefficient: 3.5
Solvent content (%): 64.83
Ligand: (3R)-3-methyl-1-(4-{[2-methyl-1-(propan-2-yl)-1H-imidazo[4,5-c]pyridin-6-yl]amino}pyrimidin-2-yl)pyrrolidine-3-carboxamide (4ZB)
Ligand formula: C20 H26 N8 O
Ligand molecular weight: 394.473
Ligand SMILES: Cc1nc2cnc(cc2n1C(C)C)Nc3ccnc(n3)N4CCC(C4)(C)C(=O)N
Ligand InChI: InChI=1S/C20H26N8O/c1-12(2)28-13(3)24-14-10-23-17(9-15(14)28)25-16-5-7-22-19(26-16)27-8-6-20(4,11-27)18(21)29/h5,7,9-10,12H,6,8,11H2,1-4H3,(H2,21,29)(H,22,23,25,26)/t20-/m1/s1
Release date: 2015-10-28
Structural basis for thymine glycosylase activity on T:O6-methylG mismatch by methyl-CpG binding domain protein 4: Implications for roles of Arg468 in mismatch recognition and catalysis (PDB entry 4OFA)
Macromolecule: Methyl-CpG-binding domain protein 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 192 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFMALSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPENHKLNKYHDWLWENHEKLSLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.13448
R free: 0.18212
Average B factor: 31.955
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 33% ethylene glycol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Matthews coefficient: 2.02
Solvent content (%): 38.98
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2015-04-22
The ATAD2 bromodomain in complex with compound 3 (PDB entry 6EPX)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.2046
R free: 0.2191
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2M ammonium sulfate, 0.1M Bis-Tris pH 5.5
Matthews coefficient: 4.09
Solvent content (%): 69.9
Ligand: (2~{R})-2-carbamimidamido-~{N}-(4-ethanoyl-1,3-thiazolidin-2-yl)propanamide (BQW)
Ligand formula: C9 H17 N5 O2 S
Ligand molecular weight: 259.329
Ligand SMILES: CC(C(=O)NC1NC(CS1)C(=O)C)NC(=N)N
Ligand InChI: InChI=1S/C9H17N5O2S/c1-4(12-8(10)11)7(16)14-9-13-6(3-17-9)5(2)15/h4,6,9,13H,3H2,1-2H3,(H,14,16)(H4,10,11,12)/t4-,6?,9?/m1/s1
Release date: 2018-10-31
Crystal structure of TNKS2 in complex with 2-[4-(piperidin-1-yl)phenyl]-3,4-dihydroquinazolin-4-one (PDB entry 5NVH)
Macromolecule: Tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 191 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.17785
R free: 0.20033
Average B factor: 25.026
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, 24/26 % PEG3350
Matthews coefficient: 2.44
Solvent content (%): 49.5
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: 2018-03-14
Crystal structure of S39D HDAC8 in complex with a largazole analogue. (PDB entry 4RN0)
Macromolecule: Histone deacetylase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 389 residues
Sequence: MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRADMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVIEGRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.761
R work: 0.1367
R free: 0.1621
Average B factor: 22.4
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Imidazole (pH=7.0), 4 mM tris(2-carboxyethyl)phosphine (TCEP), 8% PEG 8000, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Matthews coefficient: 2.47
Solvent content (%): 50.14
Ligand: (5R,8S,11S)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-3,17-dithia-7,10,14,19,20-pentaazatricyclo[14.2.1.1~2,5~]icosa-1(18),2(20),16(19)-triene-6,9,13-trione (L6G)
Ligand formula: C21 H29 N5 O3 S3
Ligand molecular weight: 495.682
Ligand SMILES: CC(C)C1C(=O)NC(CC(=O)NCc2nc(cs2)C3=NC(CS3)(C(=O)N1)C)C=CCCS
Ligand InChI: InChI=1S/C21H29N5O3S3/c1-12(2)17-18(28)23-13(6-4-5-7-30)8-15(27)22-9-16-24-14(10-31-16)19-26-21(3,11-32-19)20(29)25-17/h4,6,10,12-13,17,30H,5,7-9,11H2,1-3H3,(H,22,27)(H,23,28)(H,25,29)/b6-4+/t13-,17+,21+/m1/s1
Release date: 2015-04-08
Inhibitor of ERK2 (PDB entry 6RQ4)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.175
R free: 0.232
Average B factor: 41.782
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 291
Crystal growth procedure: 0.25M (NH4)2SO4
33% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.31
Solvent content (%): 46.74
Ligand: 6,6-dimethyl-2-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]-5-(2-morpholin-4-ylethyl)thieno[2,3-c]pyrrol-4-one (KE8)
Ligand formula: C22 H27 N7 O2 S
Ligand molecular weight: 453.56
Ligand SMILES: CC1(c2c(cc(s2)c3ccnc(n3)Nc4ccnn4C)C(=O)N1CCN5CCOCC5)C
Ligand InChI: InChI=1S/C22H27N7O2S/c1-22(2)19-15(20(30)29(22)9-8-28-10-12-31-13-11-28)14-17(32-19)16-4-6-23-21(25-16)26-18-5-7-24-27(18)3/h4-7,14H,8-13H2,1-3H3,(H,23,25,26)
Release date: 2019-12-04
Crystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound (PDB entry 9BHS)
Macromolecule: DDB1- and CUL4-associated factor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 315 residues
Sequence: GASAFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1405
R free: 0.16957
Average B factor: 16.638
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 30% PEG2000 Monoethyl Ether, 0.2 M Potassium Bromide
Matthews coefficient: 2.17
Solvent content (%): 43.33
Ligand: (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrole-3-carboxamide (A1APJ)
Ligand formula: C24 H19 Cl2 F2 N5 O2
Ligand molecular weight: 518.343
Ligand SMILES: Cn1cc(cn1)c2c(c(c[nH]2)C(=O)NC(CC(=O)N)c3ccc(c(c3)Cl)F)c4ccc(cc4F)Cl
Ligand InChI: InChI=1S/C24H19Cl2F2N5O2/c1-33-11-13(9-31-33)23-22(15-4-3-14(25)7-19(15)28)16(10-30-23)24(35)32-20(8-21(29)34)12-2-5-18(27)17(26)6-12/h2-7,9-11,20,30H,8H2,1H3,(H2,29,34)(H,32,35)/t20-/m0/s1
Release date: 2024-05-01
Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 18 (CS587) (PDB entry 6T29)
Macromolecule: Calcium/calmodulin-dependent protein kinase type 1D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 385 residues
Sequence: MARENGESSSSWKKQAEDIKKIFEFKETLGTGAFSEVVLAEEKATGKLFAVKCIPKKALKGKESSIENEIAVLRKIKHENIVALEDIYESPNHLYLVMQLVSGGELFDRIVEKGFYTEKDASTLIRQVLDAVYYLHRMGIVHRDLKPENLLYYSQDEESKIMISDFGLSKMEGKGDVMSTACGTPGYVAPEVLAQKPYSKAVDCWSIGVIAYILLCGYPPFYDENDSKLFEQILKAEYEFDSPYWDDISDSAKDFIRNLMEKDPNKRYTCEQAARHPWIAGDTALNKNIHESVSAQIRKNFAKSKWRQAFNATAVVRHMRKLHLGSSLDSSNASVSSSLSLASQKDCLAPSTLCSFISSSSGVSGVGAERRPRPTTVTAVHSGSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.484
R work: 0.1355
R free: 0.1747
Average B factor: 17.818
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.9
Crystallization temperature (K): 293
Crystal growth procedure: 0,1M NaCit, pH 5.9
2,05M AmmSO4
0,1M Na/K tartrate
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: 2019-11-13
Structure of Nedd4L WW3 domain (PDB entry 7LP1)
Macromolecule: E3 ubiquitin-protein ligase NEDD4-like
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 39 residues
Sequence: VTQSFLPPGWEMRIAPNGRPFFIDHNTKTTTWEDPRLKF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.1836
R free: 0.2135
Average B factor: 20.39
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 293.15
Crystal growth procedure: 3.6M ammonium nitrate, 5% glycerol, and 0.1M sodium acetate at pH 4.6
Matthews coefficient: 2.78
Solvent content (%): 55.73
Ligand: NITRATE ION (NO3)
Ligand formula: N O3
Ligand molecular weight: 62.005
Ligand SMILES: [N+](=O)([O-])[O-]
Ligand InChI: InChI=1S/NO3/c2-1(3)4/q-1
Release date: 2021-07-28
COMPLEMENT FACTOR D COMPLEXED WITH COMPOUND 5 (PDB entry 6FTY)
Macromolecule: Complement factor D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.46
Sequence length: 232 residues
Sequence: ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLASAAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.171
R free: 0.214
Average B factor: 14.64
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: PEG 3350, 100 mM HEPES pH 7.5
Matthews coefficient: 2.11
Solvent content (%): 41.83
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: 2018-06-06
LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (R)-N-(1-(3-isopropyl-1H-pyrazole-5-carbonyl)pyrrolidin-3-yl)cyclopropanecarboxamide (Compound N54) (PDB entry 6BH2)
Macromolecule: Lysine-specific demethylase 5A,  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): 1.447
R work: 0.1883
R free: 0.2054
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: 2.26
Solvent content (%): 45.58
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: 2018-03-28
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2447286438 (PDB entry 5RXI)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.1978
R free: 0.2343
Average B factor: 20.919
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.08
Solvent content (%): 40.96
Ligand: (3S)-N-methyl-N-phenylpyrrolidine-3-carboxamide (O3A)
Ligand formula: C12 H16 N2 O
Ligand molecular weight: 204.268
Ligand SMILES: CN(c1ccccc1)C(=O)C2CCNC2
Ligand InChI: InChI=1S/C12H16N2O/c1-14(11-5-3-2-4-6-11)12(15)10-7-8-13-9-10/h2-6,10,13H,7-9H2,1H3/t10-/m0/s1
Release date: 2020-11-11