satarupa22/MacromolecularLigandDB huggingface dataset:
CDK2-CyclinE1 in complex with allosteric inhibitor I-125A. (PDB entry 8VQ4)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1915
R free: 0.2186
Average B factor: 49.14
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 0.21 M sodium citrate tribasic dihydrate, 19.5% PEG3350
Matthews coefficient: 3
Solvent content (%): 58.94
Ligand: (8R)-6-(1-benzyl-1H-pyrazole-4-carbonyl)-N-[(2S,3R)-3-(2-cyclohexylethoxy)-1-(methylamino)-1-oxobutan-2-yl]-2-[(1S)-2,2-dimethylcyclopropane-1-carbonyl]-2,6-diazaspiro[3.4]octane-8-carboxamide (A1AC5)
Ligand formula: C37 H52 N6 O5
Ligand molecular weight: 660.846
Ligand SMILES: CC(C(C(=O)NC)NC(=O)C1CN(CC12CN(C2)C(=O)C3CC3(C)C)C(=O)c4cnn(c4)Cc5ccccc5)OCCC6CCCCC6
Ligand InChI: InChI=1S/C37H52N6O5/c1-25(48-16-15-26-11-7-5-8-12-26)31(33(45)38-4)40-32(44)30-21-41(22-37(30)23-42(24-37)35(47)29-17-36(29,2)3)34(46)28-18-39-43(20-28)19-27-13-9-6-10-14-27/h6,9-10,13-14,18,20,25-26,29-31H,5,7-8,11-12,15-17,19,21-24H2,1-4H3,(H,38,45)(H,40,44)/t25-,29-,30?,31+/m1/s1
Release date: 2024-01-31
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-048 (PDB entry 6FTW)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 364 residues
Sequence: GSHMIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.16
R work: 0.18194
R free: 0.23314
Average B factor: 47.953
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES pH 7.5
Matthews coefficient: 2.65
Solvent content (%): 53.55
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: 2019-03-20
Crystal structure of haspin (GSG2) in complex with macrocycle ODS2003128 (PDB entry 6Z5B)
Macromolecule: Serine/threonine-protein kinase haspin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 357 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMGECSQKGPVPFSHCLPTEKLQRCEKIGEGVFGEVFQTIADHTPVAIKIIAIEGPDLVNGSHQKTFEEILPEIIISKELSLLSGEVCNRTEGFIGLNSVHCVQGSYPPLLLKAWDHYNSTKGSANDRPDFFKDDQLFIVLEFEFGGIDLEQMRTKLSSLATAKSILHQLTASLAVAEASLRFEHRDLHWGNVLLKKTSLKKLHYTLNGKSSTIPSCGLQVSIIDYTLSRLERDGIVVFCDVSMDEDLFTGDGDYQFDIYRLMKKENNNRWGEYHPYSNVLWLHYLTDKMLKQMTFKTKCNTPAMKQIKRKIQEFHRTMLNFSSATDLLCQHSLFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1554
R free: 0.1977
Average B factor: 15.938
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277.15
Crystal growth procedure: 60.0% MPD, 0.1M SPG pH 7.0
Matthews coefficient: 3.09
Solvent content (%): 60.23
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: 2020-06-03
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z274575916 (PDB entry 5RY9)
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): 1.52
R work: 0.1821
R free: 0.2066
Average B factor: 16.31
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: 2.07
Solvent content (%): 40.7
Ligand: 2,4-dimethyl-6-(piperazin-1-yl)pyrimidine (WKS)
Ligand formula: C10 H16 N4
Ligand molecular weight: 192.261
Ligand SMILES: Cc1cc(nc(n1)C)N2CCNCC2
Ligand InChI: InChI=1S/C10H16N4/c1-8-7-10(13-9(2)12-8)14-5-3-11-4-6-14/h7,11H,3-6H2,1-2H3
Release date: 2020-11-11
HUMAN PI3KDELTA IN COMPLEX WITH LASW1579 (PDB entry 5M6U)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 1011 residues
Sequence: NQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPEAYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYSFPLQLEPSAQTWGPGTLRLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKATVFRQPLVEQPEDYTLQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNPAPQVQKPRAKPPPIPAKKPSSVSLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKAKKARSTKKKSKKADCPIAWANLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAPHPVYYPALEKILELGRHSECVHVTEEEQLQLREILERRGSGELYEHEKDLVWKLRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLDRALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEALSHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEAGSGGSVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLNKSNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNFKTKFGINRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRESW
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2555
R free: 0.3089
Average B factor: 110.982
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Matthews coefficient: 3.32
Solvent content (%): 62.99
Ligand: 4-azanyl-6-[[(1~{S})-1-(4-oxidanylidene-3-phenyl-pyrrolo[2,1-f][1,2,4]triazin-2-yl)ethyl]amino]pyrimidine-5-carbonitrile (7KA)
Ligand formula: C19 H16 N8 O
Ligand molecular weight: 372.383
Ligand SMILES: CC(C1=Nn2cccc2C(=O)N1c3ccccc3)Nc4c(c(ncn4)N)C#N
Ligand InChI: InChI=1S/C19H16N8O/c1-12(24-17-14(10-20)16(21)22-11-23-17)18-25-26-9-5-8-15(26)19(28)27(18)13-6-3-2-4-7-13/h2-9,11-12H,1H3,(H3,21,22,23,24)/t12-/m0/s1
Release date: 2017-02-01
Crystal structure of human glutaminyl cyclase in complex with Glu(gamma-hydrazide)-Phe-Ala (PDB entry 6YI1)
Macromolecule: Glutaminyl-peptide cyclotransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.5
Sequence length: 329 residues
Sequence: GPAWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPYGYRSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDSAVPCAMMLELARALDKKLLSLKTVSDSKPDLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.1593
R free: 0.1862
Average B factor: 30.3477
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M ammonium sulfate, 0.1M MES pH 6.5, 4% (v/v) 1,4-Dioxane
Matthews coefficient: 3.08
Solvent content (%): 60.08
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: 2020-07-01
CLK1 V324A mutant bound with benzothiazole Tg003 (Cpd 2) (PDB entry 6YTD)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 339 residues
Sequence: SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVADFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1794
R free: 0.228
Average B factor: 28.811
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 17% PEG 3350, 0,2M Na malonate
Matthews coefficient: 2.69
Solvent content (%): 54.19
Ligand: (1~{Z})-1-(3-ethyl-5-methoxy-1,3-benzothiazol-2-ylidene)propan-2-one (EAE)
Ligand formula: C13 H15 N O2 S
Ligand molecular weight: 249.329
Ligand SMILES: CCN1c2cc(ccc2SC1=CC(=O)C)OC
Ligand InChI: InChI=1S/C13H15NO2S/c1-4-14-11-8-10(16-3)5-6-12(11)17-13(14)7-9(2)15/h5-8H,4H2,1-3H3/b13-7-
Release date: 2020-07-15
Crystal structure of HOIP RING1 domain bound to IpaH1.4 LRR domain (PDB entry 7V8G)
Macromolecule: RING-type E3 ubiquitin transferase
Type: Protein, polypeptide(L)
Source organism: Shigella flexneri 5a str. M90T
EC number: 2.3.2.27
Sequence length: 240 residues
Sequence: GPGSNEFYLKTWSEWEKNGTPGEQRNIAFNRLKICLQNQEAELNLSELDLKTLPDLPPQITTLEIRKNLLTHLPDLPPMLKVIHAQFNQLESLPALPETLEELNAGDNKIKELPFLPENLTHLRVHNNRLHILPLLPPELKLLVVSGNRLDSIPPFPDKLEGLALANNFIEQLPELPFSMNRAVLMNNNLTTLPESVLRLAQNAFVNVAGNPLSGHTMRTLQQITTGPDYSGPRIFFSMG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2201
R free: 0.2781
Average B factor: 65.64
Crystallization method: EVAPORATION
Crystallization pH: 8
Crystallization temperature (K): 289
Crystal growth procedure: 2%(v/v) 1,4-dioxane, 0.1 M Tris-HCl (pH 8.0), 15%(v/v) PEG 3,350
Matthews coefficient: 2.36
Solvent content (%): 47.87
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: 2022-03-30
Rapid optimisation of fragments and hits to lead compounds from screening of crude reaction mixtures (PDB entry 6TN2)
Macromolecule: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.2
Sequence length: 394 residues
Sequence: GSAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDGSTNPAHPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVYNKSAWRHYQTIQEAGDWCVPSTEPKNTSTYRVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.768
R work: 0.1706
R free: 0.2105
Average B factor: 40.967
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Sodium acetate pH 5.8
0.125 M Magnesium chloride
Matthews coefficient: 3.19
Solvent content (%): 61.39
Ligand: N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE (TF3)
Ligand formula: C20 H25 Cl N2 O2
Ligand molecular weight: 360.878
Ligand SMILES: CC(C)c1ccc(cc1)COc2ccc(cc2Cl)CC(=O)NCCN
Ligand InChI: InChI=1S/C20H25ClN2O2/c1-14(2)17-6-3-15(4-7-17)13-25-19-8-5-16(11-18(19)21)12-20(24)23-10-9-22/h3-8,11,14H,9-10,12-13,22H2,1-2H3,(H,23,24)
Release date: 2020-10-14
Crystal structure of a PP2A B56gamma/BubR1 complex (PDB entry 5JJA)
Macromolecule: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 352 residues
Sequence: GIRDVPPADQEKLFIQKLRQCCVLFDFVSDPLSDLKWKEVKRAALSEMVEYITHNRNVITEPIYPEVVHMFAVNMFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQLVYEFFLRFLESPDFQPNIAKKYIDQKFVLQLLELFDSEDPRERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSIINGFALPLKEEHKIFLLKVLLPLHKVKSLSVYHPQLAYCVVQFLEKDSTLTEPVVMALLKYWPKTHSPKEVMFLNELEEILDVIEPSEFVKIMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDNAAKILPIMFPSLYRNSKT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1795
R free: 0.2041
Average B factor: 44.293
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES pH 7.5 and 20% PEG 3350
Matthews coefficient: 3.53
Solvent content (%): 60.25
Release date: 2016-07-13
PCSK9(deltaCRD) in complex with cyclic peptide 35 (PDB entry 7S5H)
Macromolecule: Pro-peptide from Proprotein convertase subtilisin/kexin type 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 122 residues
Sequence: QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.272
R work: 0.2056
R free: 0.2089
Average B factor: 21.53
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG3350, 200mM CaCl2, 100mM MES pH 6
Matthews coefficient: 1.76
Solvent content (%): 30.01
Ligand: (2E)-but-2-ene-1,4-diol (89N)
Ligand formula: C4 H8 O2
Ligand molecular weight: 88.105
Ligand SMILES: C(C=CCO)O
Ligand InChI: InChI=1S/C4H8O2/c5-3-1-2-4-6/h1-2,5-6H,3-4H2/b2-1+
Release date: 2021-11-03
Crystal structure of Pim-1 kinase domain in complex with 2-methyl-5-phenylfuran-3-carboxylic acid (PDB entry 4MTA)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 286 residues
Sequence: GKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1584
R free: 0.192
Average B factor: 38.94
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.4
Crystallization temperature (K): 293
Crystal growth procedure: 1.0 M ammonium dihydrogen phosphate, 0.2 M sodium chloride, 0.1 M sodium citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 3.22
Solvent content (%): 61.75
Ligand: 2-methyl-5-phenylfuran-3-carboxylic acid (2D2)
Ligand formula: C12 H10 O3
Ligand molecular weight: 202.206
Ligand SMILES: Cc1c(cc(o1)c2ccccc2)C(=O)O
Ligand InChI: InChI=1S/C12H10O3/c1-8-10(12(13)14)7-11(15-8)9-5-3-2-4-6-9/h2-7H,1H3,(H,13,14)
Release date: 2015-01-14
Crystal structure of EP300 HAT domain in complex with compound 10 (PDB entry 8GZC)
Macromolecule: Histone acetyltransferase p300
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 454 residues
Sequence: GPSLGYCCGRKLEFSPQTLCCYGKQLCTIPRDATYYSYQNRYHFCEKCFNEIQGESVSLGDDPSQPQTTINKEQFSKRKNDTLDPELFVECTECGRKMHQICVLHHEIIWPAGFVCDGCLKKSARTRKENKFSAKRLPSTRLGTFLENRVNDFLRRQNHPESGEVTVRVVHASDKTVEVKPGMKARFVDSGEMAESFPYRTKALFAFEEIDGVDLCFFGMHVQEYGSDCPPPNQRRVYISYLDSVHFFRPKCLRTAVYHEILIGYLEYVKKLGYTTGHIWACPPSEGDDYIFHCHPPDQKIPKPKRLQEWFKKMLDKAVSERIVHDYKDIFKQATEDRLTSAKELPYFEGDFWPNVLEESIKESGGSGSQKLYATMEKHKEVFFVIRLIAGPAANSLPPIVDPDPLIPCDLMDGRDAFLTLARDKHLEFSSLRRAQWSTMCMLVELHTQSQDRF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1945
R free: 0.2268
Average B factor: 65.3943
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 15% PEG3350, 0.1 M HEPES
Matthews coefficient: 3.02
Solvent content (%): 59.21
Ligand: (2~{R},4~{R})-4-fluoranyl-1-[1-(4-methoxyphenyl)cyclohexyl]carbonyl-~{N}-(1~{H}-pyrazolo[4,3-b]pyridin-5-yl)pyrrolidine-2-carboxamide (KQO)
Ligand formula: C25 H28 F N5 O3
Ligand molecular weight: 465.52
Ligand SMILES: COc1ccc(cc1)C2(CCCCC2)C(=O)N3CC(CC3C(=O)Nc4ccc5c(n4)cn[nH]5)F
Ligand InChI: InChI=1S/C25H28FN5O3/c1-34-18-7-5-16(6-8-18)25(11-3-2-4-12-25)24(33)31-15-17(26)13-21(31)23(32)29-22-10-9-19-20(28-22)14-27-30-19/h5-10,14,17,21H,2-4,11-13,15H2,1H3,(H,27,30)(H,28,29,32)/t17-,21-/m1/s1
Release date: 2023-01-11
Human CSNK2A2 bound to a Pyrrolo[2,3-d]pyrimidinyl inhibitor (PDB entry 6QY9)
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: SMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.12504
R free: 0.16477
Average B factor: 20.652
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG3350, 0.2 M potassium nitrate
Matthews coefficient: 2.24
Solvent content (%): 45.09
Ligand: 3-[3-[2-[(3,4,5-trimethoxyphenyl)amino]pyrrolo[2,3-d]pyrimidin-7-yl]phenyl]propanenitrile (JL2)
Ligand formula: C24 H23 N5 O3
Ligand molecular weight: 429.471
Ligand SMILES: COc1cc(cc(c1OC)OC)Nc2ncc3ccn(c3n2)c4cccc(c4)CCC#N
Ligand InChI: InChI=1S/C24H23N5O3/c1-30-20-13-18(14-21(31-2)22(20)32-3)27-24-26-15-17-9-11-29(23(17)28-24)19-8-4-6-16(12-19)7-5-10-25/h4,6,8-9,11-15H,5,7H2,1-3H3,(H,26,27,28)
Release date: 2019-04-17
Crystal structure of FAM46C (PDB entry 6W36)
Macromolecule: Terminal nucleotidyltransferase 5C
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.19
Sequence length: 347 residues
Sequence: MAFSVLNWDQVSRLHEVLTEVVPIHGRGNFPTLEITLKDIVQTVRSRLEEAGIKVHDVRLNGSAAGHVLVKDNGLGCKDLDLIFHVALPTEAEFQLVRDVVLCSLLNFLPEGVNKLKISPVTLKEAYVQKLVKVCTDTDRWSLISLSNKNGKNVELKFVDSIRRQFEFSVDSFQIILDSLLFFYDCSNNPISEHFHPTVIGESMYGDFEEAFDHLQNRLIATKNPEEIRGGGLLKYSNLLVRDFRPTDQEEIKTLERYMCSRFFIDFPDILEQQRKLETYLQNHFAEEERSKYDYLMILRRVVNESTVCLMGHERRQTLNLISLLALRVLAEQNIIPSATNVTCYYQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.854
R work: 0.2149
R free: 0.2591
Crystallization method: LIQUID DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 1 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 1% PEG3350
Matthews coefficient: 3.31
Solvent content (%): 62.89
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: 2020-05-06
FXIIIa in complex with the inhibitor ZED2360 (PDB entry 5MHN)
Macromolecule: Coagulation factor XIII A chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.13
Sequence length: 738 residues
Sequence: MHHHHHHSETSRTAFGGRRAVPPNNSNAAEDDLPTVELQGVVPRGVNLQEFLNVTSVHLFKERWDTNKVDHHTDKYENNKLIVRRGQSFYVQIDFSRPYDPRRDLFRVEYVIGRYPQENKGTYIPVPIVSELQSGKWGAKIVMREDRSVRLSIQSSPKCIVGKFRMYVAVWTPYGVLRTSRNPETDTYILFNPWCEDDAVYLDNEKEREEYVLNDIGVIFYGEVNDIKTRSWSYGQFEDGILDTCLYVMDRAQMDLSGRGNPIKVSRVGSAMVNAKDDEGVLVGSWDNIYAYGVPPSAWTGSVDILLEYRSSENPVRYGQCWVFAGVFNTFLRCLGIPARIVTNYFSAHDNDANLQMDIFLEEDGNVNSKLTKDSVWNYHCWNEAWMTRPDLPVGFGGWQAVDSTPQENSDGMYRCGPASVQAIKHGHVCFQFDAPFVFAEVNSDLIYITAKKDGTHVVENVDATHIGKLIVTKQIGGDGMMDITDTYKFQEGQEEERLALETALMYGAKKPLNTEGVMKSRSNVDMDFEVENAVLGKDFKLSITFRNNSHNRYTITAYLSANITFYTGVPKAEFKKETFDVTLEPLSFKKEAVLIQAGEYMGQLLEQASLHFFVTARINETRDVLAKQKSTVLTIPEIIIKVRGTQVVGSDMTVIVEFTNPLKETLRNVWVHLDGPGVTRPMKKMFREIRPNSTVQWEEVCRPWVSGHRKLIASMSSDSLRHVYGELDVQIQRRPSM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.48
R work: 0.1796
R free: 0.238
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 170 mM ammonium sulfate, 85 mM sodium cacodylate, 25.5 % PEG8000, 15 % glycerol
Matthews coefficient: 2.66
Solvent content (%): 53.75
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: 2017-12-20
Crystal structure of recombinant coagulation factor beta-XIIa (PDB entry 6GT6)
Macromolecule: Coagulation factor XII
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.38
Sequence length: 253 residues
Sequence: VVGGLVALRGAHPYIAALYWGHSFCAGSLIAPCWVLTAAHCLQDRPAPEDLTVVLGQERRNHSCEPCQTLAVRSYRLHEAFSPVSYQHDLALLRLQEDADGSCALLSPYVQPVCLPSGAARPSETTLCQVAGWGHQFEGAEEYASFLQEAQVPFLSLERCSAPDVHGSSILPGMLCAGFLEGGTDACQGDSGGPLVCEDQAAERRLTLQGIISWGSGCGDRNKPGVYTDVAYYLAWIREHTVSTRTGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.54
R work: 0.2115
R free: 0.2636
Average B factor: 40.686
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292.15
Crystal growth procedure: 0.1M Tris.Cl pH 8.0, 1.5M AmSO4
Matthews coefficient: 3.69
Solvent content (%): 66.64
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: 2019-07-17
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1493056027 (PDB entry 7G8Z)
Macromolecule: Rho guanine nucleotide exchange factor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 245 residues
Sequence: SMEMDEKDFAADSWSLAVDSSFLQQHKKEVMKQQDVIYELIQTELHHVRTLKIMTRLFRTGMLEELHLEPGVVQGLFPCVDELSDIHTRFLSQLLERRRQALCPGSTRNFVIHRLGDLLISQFSGPSAEQMCKTYSEFCSRHSKALKLYKELYARDKRFQQFIRKVTRPAVLKRHGVQECILLVTQRITKYPLLISRILQHSHGIEEERQDLTTALGLVKELLSNVDEGIYQLEKGARLQEIYNR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.509
R work: 0.1935
R free: 0.2207
Average B factor: 27.08
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.51
Solvent content (%): 50.91
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: 2023-07-12