satarupa22/MacromolecularLigandDB huggingface dataset:
Human carbonic anhydrase II in complex with Methyl 3-((4-methylthiazol-2-yl)(4-sulfamoylphenyl)amino)propanoate (PDB entry 7QGZ)
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): 1.13
R work: 0.1983
R free: 0.2173
Average B factor: 13.507
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M sodium bicine (pH 9.0), 0.2M ammonium sulfate and 2M sodium malonate (pH 7.0)
Matthews coefficient: 2.08
Solvent content (%): 40.84
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: 2022-05-04
X-ray structure of NSD3-PWWP1 in complex with compound 3 (PDB entry 6G24)
Macromolecule: Histone-lysine N-methyltransferase NSD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 136 residues
Sequence: STGVKFQVGDLVWSKVGTYPWWPCMVSSDPQLEVHTKINTRGAREYHVQFFSNQPERAWVHEKRVREYKGHKQYEELLAEATKQASNHSEKQKIRKPRPQRERAQWDIGIAHAEKALKMTREERIEQYTFIYIDKQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.202
R free: 0.235
Average B factor: 36.83
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols
Matthews coefficient: 2.3
Solvent content (%): 46.58
Ligand: 2-[(~{E})-2-thiophen-2-ylethenyl]benzoic acid (EH2)
Ligand formula: C13 H10 O2 S
Ligand molecular weight: 230.282
Ligand SMILES: c1ccc(c(c1)C=Cc2cccs2)C(=O)O
Ligand InChI: InChI=1S/C13H10O2S/c14-13(15)12-6-2-1-4-10(12)7-8-11-5-3-9-16-11/h1-9H,(H,14,15)/b8-7+
Release date: 2019-06-26
Co-complex CYP46A1 with 7742 (Soticlestat/TAK-935)) (PDB entry 7LRL)
Macromolecule: Cholesterol 24-hydroxylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.25
Sequence length: 474 residues
Sequence: MHHHHHHSRYEHIPGPPRPSFLLGHLPCFWKKDEVGGRVLQDVFLDWAKKYGPVVRVNVFHKTSVIVTSPESVKKFLMSTKYNKDSKMYRALQTVFGERLFGQGLVSECNYERWHKQRRVIDLAFSRSSLVSLMETFNEKAEQLVEILEAKADGQTPVSMQDMLTYTAMDILAKAAFGMETSMLLGAQKPLSQAVKLMLEGITASRNTLAKFLPGKRKQLREVRESIRFLRQVGRDWVQRRREALKRGEEVPADILTQILKAEEGAQDDEGLLDNFVTFFIAGHETSANHLAFTVMELSRQPEIVARLQAEVDEVIGSKRYLDFEDLGRLQYLSQVLKESLRLYPPAWGTFRLLEEETLIDGVRVPGNTPLLFSTYVMGRMDTYFEDPLTFNPDRFGPGAPKPRFTYFPFSLGHRSCIGQQFAQMEVKVVMAKLLQRLEFRLVPGQRFGLQEQATLKPLDPVLCTLRPRGWQPA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.995
R work: 0.2193
R free: 0.2365
Average B factor: 16.735
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 18.5% PEG 3350, 0.4M Calcium Cl
Matthews coefficient: 2.1
Solvent content (%): 41.51
Ligand: [4-oxidanyl-4-(phenylmethyl)piperidin-1-yl]-(2-pyridin-4-ylpyridin-3-yl)methanone (YBS)
Ligand formula: C23 H23 N3 O2
Ligand molecular weight: 373.448
Ligand SMILES: c1ccc(cc1)CC2(CCN(CC2)C(=O)c3cccnc3c4ccncc4)O
Ligand InChI: InChI=1S/C23H23N3O2/c27-22(20-7-4-12-25-21(20)19-8-13-24-14-9-19)26-15-10-23(28,11-16-26)17-18-5-2-1-3-6-18/h1-9,12-14,28H,10-11,15-17H2
Release date: 2021-08-25
Crystal Structure of human cyclic GMP-AMP synthase in complex with 2-[(2-chloro-5-pyridin-4-ylphenyl)methylamino]-5-propyl-4H-[1,2,4]triazolo[1,5-a]pyrimidin-7-one (PDB entry 7FU9)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.668
R work: 0.1949
R free: 0.2584
Average B factor: 51.1398
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals
Matthews coefficient: 2.07
Solvent content (%): 40.69
Ligand: (8S)-2-({[2-chloro-5-(pyridin-4-yl)phenyl]methyl}amino)-5-propyl[1,2,4]triazolo[1,5-a]pyrimidin-7(4H)-one (YOB)
Ligand formula: C20 H19 Cl N6 O
Ligand molecular weight: 394.857
Ligand SMILES: CCCC1=CC(=O)n2c(nc(n2)NCc3cc(ccc3Cl)c4ccncc4)N1
Ligand InChI: InChI=1S/C20H19ClN6O/c1-2-3-16-11-18(28)27-20(24-16)25-19(26-27)23-12-15-10-14(4-5-17(15)21)13-6-8-22-9-7-13/h4-11H,2-3,12H2,1H3,(H2,23,24,25,26)
Release date: 2024-02-21
Crystal structure of human Cdk12/Cyclin K in complex with inhibitor SR-4835 (PDB entry 8P81)
Macromolecule: Cyclin-dependent kinase 12
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 351 residues
Sequence: GQTESDWGKRCVDKFDIIGIIGEGTYGQVYKAKDKDTGELVALKKVRLDNEKEGFPITAIREIKILRQLIHRSVVNMKEIVTDKQDALDFKKDKGAFYLVFEYMDHDLMGLLESGLVHFSEDHIKSFMKQLMEGLEYCHKKNFLHRDIKCSNILLNNSGQIKLADFGLARLYNSEESRPYTNKVITLWYRPPELLLGEERYTPAIDVWSCGCILGELFTKKPIFQANLELAQLELISRLCGSPCPAVWPDVIKLPYFNTMKPKKQYRRRLREEFSFIPSAALDLLDHMLTLDPSKRCTAEQTLQSDFLKDVELSKMAPPDLPHWQDCHELWSKKRRRQRQSGVVVEEPPPS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.207
R free: 0.2548
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 288
Crystal growth procedure: 0.1 M MOPS pH 6.5, 30% PEG mix, 0.1 M NDSB
Matthews coefficient: 2.88
Solvent content (%): 57.3
Ligand: ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine (RMF)
Ligand formula: C21 H20 Cl2 N10 O
Ligand molecular weight: 499.356
Ligand SMILES: Cn1cc(cn1)n2cnc3c2nc(nc3NCc4[nH]c5cc(c(cc5n4)Cl)Cl)N6CCOCC6
Ligand InChI: InChI=1S/C21H20Cl2N10O/c1-31-10-12(8-26-31)33-11-25-18-19(29-21(30-20(18)33)32-2-4-34-5-3-32)24-9-17-27-15-6-13(22)14(23)7-16(15)28-17/h6-8,10-11H,2-5,9H2,1H3,(H,27,28)(H,24,29,30)
Release date: 2023-11-22
Crystal structure of mammalian Rev7 in complex with Rev3 1875-1895 (PDB entry 5O8K)
Macromolecule: Mitotic spindle assembly checkpoint protein MAD2B
Type: Protein, polypeptide(L)
Source organism: Mus musculus
Sequence length: 211 residues
Sequence: MTTLTRQDLNSAQVVADVLSEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSINSDSLLSHVEQLLRAFILKISKVDKVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKNS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2552
R free: 0.2888
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 2000 MME, 0.8M sodium formate, 0.1M tris-HCl pH 7.5
Matthews coefficient: 2.13
Solvent content (%): 42.37
Release date: 2018-06-27
Fibroblast growth factor receptor 1 kinase in complex with JK-P3 (PDB entry 4UWC)
Macromolecule: FIBROBLAST GROWTH FACTOR RECEPTOR 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: GAGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1774
R free: 0.2058
Average B factor: 51.54
Crystal growth procedure: 20% PEG8000, 20% ETHYLENE GLYCOL, 0.2M AMMONIUM SULPHATE, 0.1M PCTP PH 6.75
Matthews coefficient: 2.83
Solvent content (%): 56.5
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2015-09-02
Human CYP3A4 bound to an inhibitor (PDB entry 6DAC)
Macromolecule: Cytochrome P450 3A4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14
Sequence length: 487 residues
Sequence: MAYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDGTVSGAHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.209
R free: 0.274
Crystallization method: MICROBATCH
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: peg 3350, malonate
Matthews coefficient: 2.2
Solvent content (%): 44.11
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2019-04-03
Crystal structure of p38 alpha in complex with compound 75 (MCP33) (PDB entry 6SFI)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 361 residues
Sequence: GMSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGHRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLAQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.175
R free: 0.2025
Average B factor: 23.891
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.2
Crystallization temperature (K): 277.15
Crystal growth procedure: 25% MMW PEG smears, 0.1M MES pH 6.2
Matthews coefficient: 2.28
Solvent content (%): 46.02
Ligand: ~{N}-[(2~{S})-1-azanyl-4-cyclohexyl-1-oxidanylidene-butan-2-yl]-2-[[[1-(2-methylphenyl)pyrazol-4-yl]carbonylamino]methyl]-1,3-thiazole-5-carboxamide (LB5)
Ligand formula: C26 H32 N6 O3 S
Ligand molecular weight: 508.636
Ligand SMILES: Cc1ccccc1n2cc(cn2)C(=O)NCc3ncc(s3)C(=O)NC(CCC4CCCCC4)C(=O)N
Ligand InChI: InChI=1S/C26H32N6O3S/c1-17-7-5-6-10-21(17)32-16-19(13-30-32)25(34)29-15-23-28-14-22(36-23)26(35)31-20(24(27)33)12-11-18-8-3-2-4-9-18/h5-7,10,13-14,16,18,20H,2-4,8-9,11-12,15H2,1H3,(H2,27,33)(H,29,34)(H,31,35)/t20-/m0/s1
Release date: 2019-09-11
Crystal Structure of human phosphodiesterase 10 in complex with 2-[[4-(1-methyl-4-pyridin-4-ylpyrazol-3-yl)phenoxy]methyl]quinoline (PDB entry 5SJX)
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): 2.06
R work: 0.1799
R free: 0.2367
Average B factor: 36.839
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: 2.65
Solvent content (%): 53.58
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2022-10-12
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOOA000555a (PDB entry 5QG8)
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): 1.634
R work: 0.1858
R free: 0.2052
Average B factor: 36.9411
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: 3.35
Solvent content (%): 63.27
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: 2018-10-10
Kinase domain of mutant human ULK1 in complex with compound WZ4003 (PDB entry 8P5J)
Macromolecule: Serine/threonine-protein kinase ULK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 284 residues
Sequence: SMEPGRGGTETVGKFEFSRKDLIGHGAFAVVFKGRHREKHDLEVAVKCINKKNLAKSQTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAATLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKTLVPTIPAATSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDASPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.164
R work: 0.1676
R free: 0.2001
Average B factor: 46.156
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.3-0.8 M NaAcetate pH 6, 20-26% w/v PEG3350
Matthews coefficient: 3.42
Solvent content (%): 64.08
Ligand: ~{N}-[3-[5-chloranyl-2-[[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino]pyrimidin-4-yl]oxyphenyl]propanamide (WYT)
Ligand formula: C25 H29 Cl N6 O3
Ligand molecular weight: 496.989
Ligand SMILES: CCC(=O)Nc1cccc(c1)Oc2c(cnc(n2)Nc3ccc(cc3OC)N4CCN(CC4)C)Cl
Ligand InChI: InChI=1S/C25H29ClN6O3/c1-4-23(33)28-17-6-5-7-19(14-17)35-24-20(26)16-27-25(30-24)29-21-9-8-18(15-22(21)34-3)32-12-10-31(2)11-13-32/h5-9,14-16H,4,10-13H2,1-3H3,(H,28,33)(H,27,29,30)
Release date: 2024-06-05
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMSOA000955b (PDB entry 5QEN)
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): 1.775
R work: 0.1802
R free: 0.209
Average B factor: 41.4624
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: 3.35
Solvent content (%): 63.25
Ligand: [(3S,4R)-4-(4-fluorophenyl)-1-methylpiperidin-3-yl]methanol (JLD)
Ligand formula: C13 H18 F N O
Ligand molecular weight: 223.287
Ligand SMILES: CN1CCC(C(C1)CO)c2ccc(cc2)F
Ligand InChI: InChI=1S/C13H18FNO/c1-15-7-6-13(11(8-15)9-16)10-2-4-12(14)5-3-10/h2-5,11,13,16H,6-9H2,1H3/t11-,13-/m0/s1
Release date: 2018-10-10
Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Mn, NOG and Factor X peptide fragment (39mer-4Ser) (PDB entry 6Q9F)
Macromolecule: Aspartyl/asparaginyl beta-hydroxylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.16
Sequence length: 429 residues
Sequence: KPKLLNKFDKTIKAELDAAEKLRKRGKIEEAVNAFKELVRKYPQSPRARYGKAQCEDDLAEKRRSNEVLRGAIETYQEVASLPDVPADLLKLSLKRRSDRQQFLGHMRGSLLTLQRLVQLFPNDTSLKNDLGVGYLLIGDNDNAKKVYEEVLSVTPNDGFAKVHYGFILKAQNKIAESIPYLKEGIESGDPGTDDGRFYFHLGDAMQRVGNKEAYKWYELGHKRGHFASVWQRSLYNVNGLKAQPWWTPKETGYTELVKSLERNWKLIRDEGLAVMDKAKGLFLPEDENLREKGDWSQFTLWQQGRRNENACKGAPKTCTLLEKFPETTGCRRGQIKYSIMHPGTHVWPATGPTNCRLRMHLGLVIPKEGCKIRCANETKTWEEGKVLIFDDSFEHEVWQDASSFRLIFIVDVWHPELTPQQRRSLPAI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1812
R free: 0.1999
Average B factor: 46
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M sodium chloride 0.1 M Tris-HCl 8.0 20 % w/v PEG 6000
Matthews coefficient: 2.7
Solvent content (%): 54.5
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: 2020-01-15
Human Pin1 with cysteine sulfinic acid 113 (PDB entry 4U85)
Macromolecule: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 181 residues
Sequence: HHHHHHHHGGLVPRGSHGMADEEKLPPGWEKAMSRSSGRVYYFNHITNASQWERPSGNSSSGGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.20279
R free: 0.24479
Average B factor: 24.552
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 50mM HEPES pH 7.5
1% PEG400
1.2-1.5M Ammonium sulfate
Matthews coefficient: 2.68
Solvent content (%): 54.18
Ligand: POLYETHYLENE GLYCOL (N=34) (15P)
Ligand formula: C69 H140 O35
Ligand molecular weight: 1529.829
Ligand SMILES: COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
Ligand InChI: InChI=1S/C69H140O35/c1-71-4-5-73-8-9-75-12-13-77-16-17-79-20-21-81-24-25-83-28-29-85-32-33-87-36-37-89-40-41-91-44-45-93-48-49-95-52-53-97-56-57-99-60-61-101-64-65-103-68-69-104-67-66-102-63-62-100-59-58-98-55-54-96-51-50-94-47-46-92-43-42-90-39-38-88-35-34-86-31-30-84-27-26-82-23-22-80-19-18-78-15-14-76-11-10-74-7-6-72-3-2-70/h70H,2-69H2,1H3
Release date: 2015-04-08
Structure of WT RET protein tyrosine kinase domain at 1.92A resolution. (PDB entry 6NJA)
Macromolecule: Proto-oncogene tyrosine-protein kinase receptor Ret
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 314 residues
Sequence: GPLSLSVDAFKILEDPKWEFPRKNLVLGKTLGEGEFGKVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQVNHPHVIKLYGACSQDGPLLLIVEYAKYGSLRGFLRESRKVGPGYLGSGGSRNSSSLDHPDERALTMGDLISFAWQISQGMQYLAEMKLVHRDLAARNILVAEGRKMKISDFGLSRDVYEEDSYVKRSQGRIPVKWMAIESLFDHIYTTQSDVWSFGVLLWEIVTLGGNPYPGIPPERLFNLLKTGHRMERPDNCSEEMYRLMLQCWKQEPDKRPVFADISKDLEKMMVKRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.1832
R free: 0.234
Average B factor: 41.276
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 295
Crystal growth procedure: 2.2-2.6M Na FORMATE, 0.1m Na CITRATE pH5.5
Matthews coefficient: 2.78
Solvent content (%): 55.79
Ligand: ADENINE (ADE)
Ligand formula: C5 H5 N5
Ligand molecular weight: 135.127
Ligand SMILES: c1[nH]c2c(n1)c(ncn2)N
Ligand InChI: InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)
Release date: 2019-06-05
CRYSTAL STRUCTURE OF THE PTPN4 PDZ DOMAIN COMPLEXED WITH THE TAILORED PEPTIDE CYTO8-RETEV (PDB entry 5EYZ)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 107 residues
Sequence: GSSPEKPTPNGGIPHDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.2291
R free: 0.2395
Average B factor: 65.36
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 23% PEG 8000, 0.1 M MES PH 6.0, 0.2 M CALCIUM ACETATE, 0.143 MM AMMONIUM SULFATE
Matthews coefficient: 3.37
Solvent content (%): 63.55
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: 2016-06-08
Thrombin in complex with 4-amino-N-(5-methylisoxazol-3-yl)benzenesulfonamide (j80) (PDB entry 6YSX)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.48
R work: 0.1334
R free: 0.1617
Average B factor: 26.2084
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20mM sodium dihydrogen phosphate pH 7.5
350mM NaCl
27% PEG 8000
Matthews coefficient: 2.77
Solvent content (%): 55.7
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2021-05-12