satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of CaMKK2 in complex with CKI-012 (PDB entry 5YVC)
Macromolecule: Calcium/calmodulin-dependent protein kinase kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 298 residues
Sequence: GSSGSSGDCVQLNQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAGFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNTVGTPAFMAPESLSETRKIFSGKALDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.1701
R free: 0.2111
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M sodium cocodylate pH 6.0, 0.2M sodium acetate, 20% PEG 8000, 0.03M xylitol
Matthews coefficient: 3.23
Solvent content (%): 61.94
Ligand: 3-{2,4-dimethyl-5-[(Z)-(2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-1H-pyrrol-3-yl}propanoic acid (SU6)
Ligand formula: C18 H18 N2 O3
Ligand molecular weight: 310.347
Ligand SMILES: Cc1c(c([nH]c1C=C2c3ccccc3NC2=O)C)CCC(=O)O
Ligand InChI: InChI=1S/C18H18N2O3/c1-10-12(7-8-17(21)22)11(2)19-16(10)9-14-13-5-3-4-6-15(13)20-18(14)23/h3-6,9,19H,7-8H2,1-2H3,(H,20,23)(H,21,22)/b14-9-
Release date: 2018-12-05
CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH ACTIVE SITE INHIBITOR GRL-8234 AND EXOSITE PEPTIDE (PDB entry 5MCO)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 409 residues
Sequence: ETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVASIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.49
R work: 0.17494
R free: 0.22287
Average B factor: 33.492
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 295
Crystal growth procedure: 0.1M ammonium acetate, 0.1M sodium acetate, 15% (w/v) PEG4000
Matthews coefficient: 3.98
Solvent content (%): 69.1
Ligand: N-{(1S,2R)-1-benzyl-2-hydroxy-3-[(3-methoxybenzyl)amino]propyl}-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide (BSD)
Ligand formula: C36 H42 N4 O6 S
Ligand molecular weight: 658.807
Ligand SMILES: CC(c1ccccc1)NC(=O)c2cc(cc(c2)N(C)S(=O)(=O)C)C(=O)NC(Cc3ccccc3)C(CNCc4cccc(c4)OC)O
Ligand InChI: InChI=1S/C36H42N4O6S/c1-25(28-15-9-6-10-16-28)38-35(42)29-20-30(22-31(21-29)40(2)47(4,44)45)36(43)39-33(19-26-12-7-5-8-13-26)34(41)24-37-23-27-14-11-17-32(18-27)46-3/h5-18,20-22,25,33-34,37,41H,19,23-24H2,1-4H3,(H,38,42)(H,39,43)/t25-,33+,34-/m1/s1
Release date: 2017-09-27
Crystal Structure of human phosphodiesterase 10 in complex with 4-(azetidine-1-carbonyl)-N-(6-cyano-2-phenylimidazo[1,2-a]pyridin-7-yl)-2-methylpyrazole-3-carboxamide (PDB entry 5SI6)
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
R work: 0.1846
R free: 0.2214
Average B factor: 34.542
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: 2.64
Solvent content (%): 53.38
Ligand: 4-(azetidine-1-carbonyl)-N-[(4R)-6-cyano-2-phenylimidazo[1,2-a]pyridin-7-yl]-1-methyl-1H-pyrazole-5-carboxamide (JME)
Ligand formula: C23 H19 N7 O2
Ligand molecular weight: 425.443
Ligand SMILES: Cn1c(c(cn1)C(=O)N2CCC2)C(=O)Nc3cc4nc(cn4cc3C#N)c5ccccc5
Ligand InChI: InChI=1S/C23H19N7O2/c1-28-21(17(12-25-28)23(32)29-8-5-9-29)22(31)27-18-10-20-26-19(15-6-3-2-4-7-15)14-30(20)13-16(18)11-24/h2-4,6-7,10,12-14H,5,8-9H2,1H3,(H,27,31)
Release date: 2022-10-12
Masking thiol reactivity with thioamide-based MBPs- carbonic anhydrase II complexed with benzo[d]thiazole-2(3H)-thione (PDB entry 8FAL)
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): 1.37
R work: 0.1897
R free: 0.2224
Average B factor: 18.02
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: 2.08
Solvent content (%): 40.84
Ligand: MERCURIBENZOIC ACID (MBO)
Ligand formula: C7 H5 Hg O2
Ligand molecular weight: 321.703
Ligand SMILES: c1cc(ccc1C(=O)O)[Hg]
Ligand InChI: InChI=1S/C7H5O2.Hg/c8-7(9)6-4-2-1-3-5-6;/h2-5H,(H,8,9);
Release date: 2023-03-01
Structure of the stapled peptide YS-02 bound to MDM2 (PDB entry 4UD7)
Macromolecule: MDM2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 114 residues
Sequence: GPLGSSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDAAQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSDSGTSVSEN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.13846
R free: 0.17838
Average B factor: 23.018
Crystallization pH: 4
Crystal growth procedure: 0.1 M SODIUM CITRATE PH 4.0 AND 15 % PEG8000
Matthews coefficient: 2.8
Solvent content (%): 56
Release date: 2016-01-13
Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) (PDB entry 6BX8)
Macromolecule: Trypsin-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.4
Sequence length: 224 residues
Sequence: IVGGYTCEENSLPYQVSLNSGSHFCGGSLISEQWVVSAAHCYKTRIQVRLGEHNIKVLEGNEQFINAAKIIRHPKYNRDTLDNDIMLIKLSSPAVINARVSTISLPTAPPAAGTECLISGWGNTLSFGADYPDELKCLDAPVLTQAECKASYPGKITNSMFCVGFLEGGKDSCQRDAGGPVVCNGQLQGVVSWGHGCAWKNRPGVYTKVYNYVDWIKDTIAANS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1922
R free: 0.2211
Average B factor: 30.0686
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 298
Crystal growth procedure: 0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)
Matthews coefficient: 2.04
Solvent content (%): 39.64
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: 2019-02-06
crystal structure of SESTD2 in complex with H3.3S31phK36M peptide (PDB entry 6J9J)
Macromolecule: Histone-lysine N-methyltransferase SETD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 257 residues
Sequence: PSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERAKNKSHRDIKRMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.1891
R free: 0.2056
Average B factor: 31.201
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M potassium thiocyanate, 0.1M Bis-Tris propane,20% PEG 3350
Matthews coefficient: 3.03
Solvent content (%): 59.4
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: 2020-02-26
Novel Imidazo[1,2-a]pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity (PDB entry 5M7M)
Macromolecule: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.39
Sequence length: 871 residues
Sequence: MARRSSFQSCQIISLFTFAVGVNICLGFTAHRIKRAEGWEEGPPTVLSDSPWTNISGSCKGRCFELQEAGPPDCRCDNLCKSYTSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLARGDCCTNYQVVCKGESHWVDDDCEEIKAAECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHSPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDATFHLRGREKFNHRWWGGQPLWITATKQGVKAGTFFWSVVIPHERRILTILQWLTLPDHERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKIVGQLMDGLKQLKLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRSKFSNNAKYDPKAIIANLTCKKPDQHFKPYLKQHLPKRLHYANNRRIEDIHLLVERRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYKTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPEEVTRPNYPGIMYLQSDFDLGCTCDDKNKLDELNKRLHTKGSTEERHLLYGRPAVLYRTRYDILYHTDFESGYSEIFLMPLWTSYTVSKQAEVSSVPDHLTSCVRPDVRVSPSFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWNYFQRVLVKKYASERNGVNVISGPIFDYDYDGLHDTEDKIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNEESCNSSEDESKWVEELMKMHTARVRDIEHLTSLDFFRKTSRSYPEILTLKTYLHTYESEILVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.22896
R free: 0.28426
Average B factor: 25.371
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG3350 25%, 0.2M thiocyanate, 0.1M ammonium iodide
Matthews coefficient: 2.4
Solvent content (%): 48.67
Ligand: ~{N}-[6-[1-[3-(dimethylamino)propylsulfonyl]piperidin-4-yl]-2-ethyl-imidazo[1,2-a]pyridin-3-yl]-4-(4-fluorophenyl)-~{N}-methyl-1,3-thiazol-2-amine (7HR)
Ligand formula: C29 H37 F N6 O2 S2
Ligand molecular weight: 584.771
Ligand SMILES: CCc1c(n2cc(ccc2n1)C3CCN(CC3)S(=O)(=O)CCCN(C)C)N(C)c4nc(cs4)c5ccc(cc5)F
Ligand InChI: InChI=1S/C29H37FN6O2S2/c1-5-25-28(34(4)29-32-26(20-39-29)22-7-10-24(30)11-8-22)36-19-23(9-12-27(36)31-25)21-13-16-35(17-14-21)40(37,38)18-6-15-33(2)3/h7-12,19-21H,5-6,13-18H2,1-4H3
Release date: 2017-08-30
Complex structure of INADL PDZ89 and PLCb4 C-terminal CC-PBM (PDB entry 6IRD)
Macromolecule: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 3.1.4.11
Sequence length: 266 residues
Sequence: EGELIPQVRIEDLKQMAAYLAHLAAQQAELNSLKAAHAAEHSTMQKLHCTQVDKIVAQYDKEKSTHEKILEKAMKKKGGSNCLEIKKETEIKIQTLTTDHKSKVKEIVAQHTKEWSEMINTHSAEEQEIRDLHLSQQCELLRKLLINAHEQQTQQLKLSHDRESKEMRAHQAKISMENSKAISQDKSIKNKAERERRVRELNSSNTKKFLEERKRLAMKQSKEMDQLKKVQLEHLEFLEKQNEQAKEMQQMVKLEAEMDRRPATVV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.813
R work: 0.244
R free: 0.3022
Average B factor: 28.8551
Crystallization method: LIQUID DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.2M MgCl2, 0.1M BIS-TRIS pH6.5, 20% w/v Polyethylene glycol 3350
Matthews coefficient: 2.61
Solvent content (%): 52.86
Ligand: GOLD ION (AU)
Ligand formula: Au
Ligand molecular weight: 196.967
Ligand SMILES: [Au+]
Ligand InChI: InChI=1S/Au/q+1
Release date: 2019-01-23
Homo sapiens Get3 in complex with the Get1 cytoplasmic domain (PDB entry 8CQZ)
Macromolecule: ATPase ASNA1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6
Sequence length: 360 residues
Sequence: GAMAAGVAGWGVEAEEFEDAPDVEPLEPTLSNIIEQRSLKWIFVGGKGGVGKTTCSCSLAVQLSKGRESVLIISTDPAHNISDAFDQKFSKVPTKVKGYDNLFAMEIDPSLGVAELPDEFFEEDNMLSMGKKMMQEAMSAFPGIDEAMSYAEVMRLVKGMNFSVVVFDTAPTGHTLRLLNFPTIVERGLGRLMQIKNQISPFISQMCNMLGLGDMNADQLASKLEETLPVIRSVSEQFKDPEQTTFICVCIAEFLSLYETERLIQELAKCKIDTHNIIVNQLVFPDPEKPCKMCEARHKIQAKYLDQMEDLYEDFHIVKLPLLPHEVRGADKVNTFSALLLEPYKPPSAQGSWSHPQFEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2424
R free: 0.2832
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 44 % (v/v) 1,2-propanediol, 0.05 M calcium acetate and 0.1 M sodium acetate (pH 5.0)
Matthews coefficient: 2.7
Solvent content (%): 54.43
Release date: 2023-11-29
Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening (PDB entry 8JVD)
Macromolecule: Ubiquitin-conjugating enzyme E2 T
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 156 residues
Sequence: GSMQRASRLKRELHMLATEPPPGITCWQDKDQMDDLRAQILGGANTPYEKGVFKLEVIIPERYPFEPPQIRFLTPIYHPNIDSAGRICLDVLKLPPKGAWRPSLNIATVLTSIQLLMSEPNPDDPLMADISSEFKYNKPAFLKNARQWTEKHARQK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.696
R work: 0.2276
R free: 0.255
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 3.5M sodium formate pH 7.0
Matthews coefficient: 3.82
Solvent content (%): 67.83
Ligand: 5-fluoranyl-1,3-benzoxazol-2-amine (V2R)
Ligand formula: C7 H5 F N2 O
Ligand molecular weight: 152.126
Ligand SMILES: c1cc2c(cc1F)nc(o2)N
Ligand InChI: InChI=1S/C7H5FN2O/c8-4-1-2-6-5(3-4)10-7(9)11-6/h1-3H,(H2,9,10)
Release date: 2024-02-28
ATAD2 in complex with 1-Methyl-2-quinolone (PDB entry 7PX5)
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): 2.18
R work: 0.2064
R free: 0.2461
Average B factor: 32.33
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
Matthews coefficient: 4.08
Solvent content (%): 69.86
Ligand: 1-METHYLQUINOLIN-2(1H)-ONE (12Q)
Ligand formula: C10 H9 N O
Ligand molecular weight: 159.185
Ligand SMILES: CN1c2ccccc2C=CC1=O
Ligand InChI: InChI=1S/C10H9NO/c1-11-9-5-3-2-4-8(9)6-7-10(11)12/h2-7H,1H3
Release date: 2022-11-02
Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker (PDB entry 8UQA)
Macromolecule: E3 ubiquitin-protein ligase RNF168,Ubiquitin-conjugating enzyme E2 D3,Histone H2B type 2-E,Histone H2A type 1-B/E
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 447 residues
Sequence: GHMALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTRYHTRRNSLVNVELWTIIQKHYPRECKLRASGSGSGSGSALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAMGSGGSGGSGSGSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.049
R work: 0.192
R free: 0.2305
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 288
Crystal growth procedure: Crystals were obtained by mixing 2 microliters of the protein fusion (8.0 mg/mL) in 10 mM HEPES, pH 7.5, 600 mM NaCl, 1 mM TCEP and 2 microliters of the reservoir solution containing 0.1 M HEPES, pH 7.5, 2.4 M NaCl
Matthews coefficient: 2.69
Solvent content (%): 54.31
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2024-01-17
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z1827898537 (PDB entry 5RX2)
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): 1.27
R work: 0.171
R free: 0.1945
Average B factor: 18.179
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: 2.09
Solvent content (%): 41.26
Ligand: (3R)-N-benzylpyrrolidin-3-amine (WP4)
Ligand formula: C11 H16 N2
Ligand molecular weight: 176.258
Ligand SMILES: c1ccc(cc1)CNC2CCNC2
Ligand InChI: InChI=1S/C11H16N2/c1-2-4-10(5-3-1)8-13-11-6-7-12-9-11/h1-5,11-13H,6-9H2/t11-/m1/s1
Release date: 2020-11-11
Crystal structure of the inhibitor-free form of the serine protease kallikrein-4 (PDB entry 6NVB)
Macromolecule: Kallikrein-4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 224 residues
Sequence: IINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEADQEPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGQDQKDSCNGDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.636
R work: 0.1541
R free: 0.1803
Average B factor: 21.54
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M lithium sulfate, 0.1M sodium acetate, 22% PEG 8000
cryoprotectant = 1:1 glycerol : mother liquor
Matthews coefficient: 2.42
Solvent content (%): 49.23
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
The crystal structure of mouse PP1G in complex with truncated human PPP1R15B (631-669) (PDB entry 4V0W)
Macromolecule: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 44 residues
Sequence: GAMDPGRHTHVKRKKVTFLEEVTEYYISGDEDRKGPWEEFARDG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1727
R free: 0.2029
Crystallization pH: 7.5
Crystal growth procedure: 3 M NACL, 0.1 M HEPES, PH7.5
Matthews coefficient: 2.64
Solvent content (%): 53.49
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: 2015-03-25
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOOA000611a (PDB entry 5QGD)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.661
R work: 0.1922
R free: 0.2322
Average B factor: 39.8105
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.33
Solvent content (%): 63.05
Ligand: (1R,3R,4S)-3-(methoxymethyl)-2-(methylsulfonyl)-2-azabicyclo[2.2.2]octan-4-ol (JKJ)
Ligand formula: C10 H19 N O4 S
Ligand molecular weight: 249.327
Ligand SMILES: COCC1C2(CCC(N1S(=O)(=O)C)CC2)O
Ligand InChI: InChI=1S/C10H19NO4S/c1-15-7-9-10(12)5-3-8(4-6-10)11(9)16(2,13)14/h8-9,12H,3-7H2,1-2H3/t8-,9-,10-/m1/s1
Release date: 2018-10-10
human POGLUT1 in complex with human Notch1 EGF12 S458T mutant and UDP (PDB entry 5UB5)
Macromolecule: Neurogenic locus notch homolog protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 42 residues
Sequence: GSDVNECVTNPCQNDATCLDQIGEFQCICMPGYEGVHCEVNT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.089
R work: 0.1526
R free: 0.1931
Average B factor: 32.9548
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 20% (v/v) PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% (v/v) 2-methyl-2,4-pentanediol
Matthews coefficient: 2.36
Solvent content (%): 47.79
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2017-08-09
Anaplastic lymphoma kinase catalytic domain complexed with pyrazolopyrimidine derivative of LDK378 (PDB entry 4Z55)
Macromolecule: ALK tyrosine kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 339 residues
Sequence: ELQSPEYKLSKLRTSTIMTDYNPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRAGYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVEEEEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1843
R free: 0.2081
Average B factor: 20.63
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.6
Crystallization temperature (K): 277
Crystal growth procedure: citric acid, bis-tris propane, PEG3350
Matthews coefficient: 2.04
Solvent content (%): 39.83
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: 2016-02-03