satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the human METTL3-METTL14 complex bound to Compound 10 (ADO_AD_022) (PDB entry 7O0P)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2021
R free: 0.2625
Average B factor: 55.57
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.17
Solvent content (%): 43.26
Ligand: 4-[4-[(4,4-dimethylpiperidin-1-yl)methyl]phenyl]-9-[6-(methylamino)pyrimidin-4-yl]-1,4,9-triazaspiro[5.5]undecan-2-one (UXZ)
Ligand formula: C27 H39 N7 O
Ligand molecular weight: 477.645
Ligand SMILES: CC1(CCN(CC1)Cc2ccc(cc2)N3CC(=O)NC4(C3)CCN(CC4)c5cc(ncn5)NC)C
Ligand InChI: InChI=1S/C27H39N7O/c1-26(2)8-12-32(13-9-26)17-21-4-6-22(7-5-21)34-18-25(35)31-27(19-34)10-14-33(15-11-27)24-16-23(28-3)29-20-30-24/h4-7,16,20H,8-15,17-19H2,1-3H3,(H,31,35)(H,28,29,30)
Release date: 2021-09-15
Crystal structure of the human METTL3-METTL14 complex with compound UOZ040b (PDB entry 7OEG)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.79
R work: 0.1978
R free: 0.2697
Average B factor: 47.28
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.13
Solvent content (%): 42.37
Ligand: (R)-4-((2-azaspiro[3.3]heptan-2-yl)methyl)-N-((1-(6-(benzylamino)pyrimidin-4-yl)-3-hydroxypiperidin-3-yl)methyl)benzamide (UEE)
Ligand formula: C31 H38 N6 O2
Ligand molecular weight: 526.672
Ligand SMILES: c1ccc(cc1)CNc2cc(ncn2)N3CCCC(C3)(CNC(=O)c4ccc(cc4)CN5CC6(C5)CCC6)O
Ligand InChI: InChI=1S/C31H38N6O2/c38-29(26-10-8-25(9-11-26)18-36-20-30(21-36)12-4-13-30)33-19-31(39)14-5-15-37(22-31)28-16-27(34-23-35-28)32-17-24-6-2-1-3-7-24/h1-3,6-11,16,23,39H,4-5,12-15,17-22H2,(H,33,38)(H,32,34,35)/t31-/m1/s1
Release date: 2021-10-20
crystal structure of human REV7-RAN complex (PDB entry 6NIF)
Macromolecule: hREV7, GTP-binding nuclear protein Ran, hREV3 fusion
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 260 residues
Sequence: GTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLAAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKGSGSGSGSGSGSGSGSGSGSGSKLIGDPNLEFVAMPALAPPASREEIMATL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.002
R work: 0.2264
R free: 0.2658
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 100 mM HEPES, pH 7.0, 1.1 M sodium malonate, 0.5% Jeffamine ED-2001
Matthews coefficient: 2.38
Solvent content (%): 48.39
Release date: 2019-09-11
Thrombin in complex with 5-chlorothiophene-2-carboxamide (PDB entry 4UD9)
Macromolecule: Thrombin heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 259 residues
Sequence: IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.124
R work: 0.1254
R free: 0.1408
Average B factor: 20.1
Crystallization pH: 7.5
Crystal growth procedure: SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
Matthews coefficient: 2.5
Solvent content (%): 50.8
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2015-08-26
co-crystal structure of non-carboxylic acid inhibitor with PHD2 (PDB entry 8J1K)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 218 residues
Sequence: PALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.451
R work: 0.242
R free: 0.3084
Average B factor: 76.018
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M NH4 phosphate monobasic,0.1M Tris,8.5,50% MPD
Matthews coefficient: 2.7
Solvent content (%): 54.48
Ligand: N-[(6-cyanopyridin-3-yl)methyl]-5-oxidanyl-2-[(3R)-3-oxidanylpyrrolidin-1-yl]-1,7-naphthyridine-6-carboxamide (SY6)
Ligand formula: C20 H18 N6 O3
Ligand molecular weight: 390.395
Ligand SMILES: c1cc(ncc1CNC(=O)c2c(c3ccc(nc3cn2)N4CCC(C4)O)O)C#N
Ligand InChI: InChI=1S/C20H18N6O3/c21-7-13-2-1-12(8-22-13)9-24-20(29)18-19(28)15-3-4-17(25-16(15)10-23-18)26-6-5-14(27)11-26/h1-4,8,10,14,27-28H,5-6,9,11H2,(H,24,29)/t14-/m1/s1
Release date: 2024-04-17
TYK2 JH2 bound to Compound7 (PDB entry 8TB5)
Macromolecule: Non-receptor tyrosine-protein kinase TYK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 326 residues
Sequence: AHHHHHHHHHHGALEVLFQGPGARASPRTLNLSQLSFHRVDQKEITQLSHLGQGTRTNVYEGRLRVEGSGDPEEGKMDDEDPLVPGRDRGQELRVVLKVLDPSHHDIALAFYETASLMSQVSHTHLAFVHGVCVRGPENIMVTEYVEHGPLDVWLRRERGHVPMAWKMVVAQQLASALSYLENKNLVHGNVCGRNILLARLGLAEGTSPFIKLSDPGVGLGALSREERVERIPWLAPECLPGGANSLSTAMDKWGFGATLLEICFDGEAPLQSRSPSEKEHFYQRQHRLPEPSCPQLATLTSQCLTYEPTQRPSFRTILRDLTRLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.32
R work: 0.1842
R free: 0.2434
Average B factor: 40.01
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% w/v PEG4,000, 200mM Sodium Acetate, 100mM Tris-HCl pH8.5
Matthews coefficient: 2.06
Solvent content (%): 40.29
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2023-10-18
Crystal structure of ERK1 covalently bound to SM1-71 (PDB entry 6GES)
Macromolecule: Mitogen-activated protein kinase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 380 residues
Sequence: SMAAAAAQGGGGGEPRRTEGVGPGVPGEVEMVKGQPFDVGPRYTQLQYIGEGAYGMVSSAYDHVRKTRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRASTLEAMRDVYIVQDLMETDLYKLLKSQQLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALAHPYLEQYYDPTDEPVAEEPFTFAMELDDLPKERLKELIFQETARFQPGVLEAP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.16954
R free: 0.21261
Average B factor: 45.749
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277.14
Crystal growth procedure: 34% PEG 4k, 0.2M Li2SO4, 0.1M tris 7.5
Matthews coefficient: 2.18
Solvent content (%): 43.69
Ligand: N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]phenyl}propanamide (6H3)
Ligand formula: C24 H28 Cl N7 O
Ligand molecular weight: 465.978
Ligand SMILES: CCC(=O)Nc1ccccc1Nc2c(cnc(n2)Nc3ccc(cc3)N4CCN(CC4)C)Cl
Ligand InChI: InChI=1S/C24H28ClN7O/c1-3-22(33)28-20-6-4-5-7-21(20)29-23-19(25)16-26-24(30-23)27-17-8-10-18(11-9-17)32-14-12-31(2)13-15-32/h4-11,16H,3,12-15H2,1-2H3,(H,28,33)(H2,26,27,29,30)
Release date: 2019-02-27
Human FXIa in complex with small molecule inhibitors. (PDB entry 4D7G)
Macromolecule: COAGULATION FACTOR XIA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 238 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQAEIAEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYADSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.2242
R free: 0.2489
Average B factor: 70.57
Crystallization pH: 8.5
Crystal growth procedure: 2M AMMONIUM SULFATE, 0.1M TRIS-CL PH 8.5, 0.2M NACL
Matthews coefficient: 2.75
Solvent content (%): 55.34
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: 2016-01-20
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000530a (PDB entry 7GT6)
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): 1.66
R work: 0.1996
R free: 0.2276
Average B factor: 37.388
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.34
Solvent content (%): 63.19
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
Abl1 SH3 pTyr89/134 (PDB entry 5NP2)
Macromolecule: Tyrosine-protein kinase ABL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 61 residues
Sequence: GSHMNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1891
R free: 0.2219
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.8 M sodium citrate, 0.1 M sodium cacodylate
Matthews coefficient: 2.12
Solvent content (%): 41.91
Release date: 2018-05-16
HIF prolyl hydroxylase 2 (PHD2-R281C/V314C) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-2) (PDB entry 5LA9)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 252 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPAMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLICHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHCDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERAAAKVKYLTGEKGVRVELNKPSDSVGKDVF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.813
R work: 0.2513
R free: 0.2785
Average B factor: 37.7
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES pH 7.5, 2.0 M ammonium sulfate
Matthews coefficient: 3.04
Solvent content (%): 59.61
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: 2016-08-31
Crystal structure of EphA7 mutant G656E (PDB entry 7EEF)
Macromolecule: Ephrin type-A receptor 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 304 residues
Sequence: HFKFPGTKTYIDPETYEDPNRAVHQFAKELDASCIKIERVIGAGEFGEVCSGRLKLPEKRDVAVAIKTLKVGYTEKQRRDFLCEASIMGQFDHPNVVHLEGVVTRGKPVMIVIEFMENGALDAFLRKHDGQFTVIQLVGMLRGIAAGMRYLADMGYVHRDLAARNILVNSNLVCKVSDFGLSRVIEDDPEAVYTTTGGKIPVRWTAPEAIQYRKFTSASDVWSYGIVMWEVMSYGERPYWDMSNQDVIKAIEEGYRLPAPMDCPAGLHQLMLDCWQKERAERPKFEQIVGILDKMIRNPNSAHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.244
R free: 0.2797
Average B factor: 26.474
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295.15
Crystal growth procedure: PEG3350, Ammonium sulphate, HEPES
Matthews coefficient: 2.37
Solvent content (%): 48.18
Release date: 2021-07-07
PCSK9 in complex with compound 19 (PDB entry 7S5G)
Macromolecule: Propeptide of Proprotein convertase subtilisin/kexin type 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 122 residues
Sequence: QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.041
R work: 0.2274
R free: 0.2856
Average B factor: 26.68
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: 2.34
Solvent content (%): 47.35
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: 2021-11-03
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 1-diphosphoinositol pentakisphosphate (1-IP7) and Mg (PDB entry 6WO9)
Macromolecule: Diphosphoinositol polyphosphate phosphohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.52
Sequence length: 169 residues
Sequence: HHHHHHSSGVDLGTENLYFQSMMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.181
R free: 0.2282
Average B factor: 26.03
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 10% (w/v) PEG 8000, 10% (v/v) isopropanol, 200 mM Li2SO4, 75 mM NaAc, pH 5.5 and 25 mM HEPES, pH 7.0 and soaking in solution of 200 mM Li2SO4, 25% (w/v) PEG 8000, 10% (v/v) isopropanol, 75mM NaAc, pH 5.5, 25 mM HEPES, pH 7.0, 20 mM MgCl2 and 80 mM NaF in present of 4mM 1-IP7
Matthews coefficient: 2.26
Solvent content (%): 45.55
Ligand: (1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate (O81)
Ligand formula: C6 H19 O27 P7
Ligand molecular weight: 740.015
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C6H19O27P7/c7-34(8,9)27-1-2(28-35(10,11)12)4(30-37(16,17)18)6(32-40(25,26)33-39(22,23)24)5(31-38(19,20)21)3(1)29-36(13,14)15/h1-6H,(H,25,26)(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3+,4-,5-,6-/m1/s1
Release date: 2021-03-03
Crystal structure of KIT1 in complex with DP2976 via co-crystallization (PDB entry 6MOB)
Macromolecule: Mast/stem cell growth factor receptor Kit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 312 residues
Sequence: NNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKTSPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.181
R free: 0.21
Average B factor: 25.35
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 12 mg/mL Kit1 protein in 20 mM Tris pH 8.0, 0.25 M sodium chloride, 5 mM imidazole, 5 mM DTT, 1 mM EDTA, crystallant: 2.5 M ammonium nitrate, 0.1 M sodium acetate, pH 4.6, 5-fold molar excess DP2976, Crystal ID 204905d1
Matthews coefficient: 3.34
Solvent content (%): 63.2
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: 2019-07-31
High-resolution crystal structure of ERAP1 with bound phosphinic transition-state analogue inhibitor (PDB entry 6Q4R)
Macromolecule: Endoplasmic reticulum aminopeptidase 1,Endoplasmic reticulum aminopeptidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11
Sequence length: 912 residues
Sequence: MVFLPLKWSLATMSFLLSSLLALLTVSTPSWCQSTEASPKRSDGTPFPWNKIRLPEYVIPVHYDLLIHANLTTLTFWGTTKVEITASQPTSTIILHSHHLQISRATLRKGAGERLSEEPLQVLEHPRQEQIALLAPEPLLVGLPYTVVIHYAGNLSETFHGFYKSTYRTKEGELRILASTQFEPTAARMAFPCFDEPAFKASFSIKIRREPRHLAISNMPLVKSVTVAEGLIEDHFDVTVKMSTYLVAFIISDFESVSKITKSGVKVSVYAVPDKINQADYALDAAVTLLEFYEDYFSIPYPLPKQDLAAIPDFQSGAMENWGLTTYRESALLFDAEKSSASSKLGITMTVAHELAHQWFGNLVTMEWWNDLWLNEGFAKFMEFVSVSVTHPELKVGDYFFGKCFDAMEVDALNSSHPVSTPVENPAQIREMFDDVSYDKGACILNMLREYLSADAFKSGIVQYLQKHSYKNTKNEDLWDSMASIGSGGVDVKTMMNTWTLQKGFPLITITVRGRNVHMKQEHYMKGSDGAPDTGYLWHVPLTFITSKSDMVHRFLLKTKTDVLILPEEVEWIKFNVGMNGYYIVHYEDDGWDSLTGLLKGTHTAVSSNDRASLINNAFQLVSIGKLSIEKALDLSLYLKHETEIMPVFQGLNELIPMYKLMEKRDMNEVETQFKAFLIRLLRDLIDKQTWTDEGSVSERMLRSQLLLLACVHNYQPCVQRAEGYFRKWKESNGNLSLPVDVTLAVFAVGAQSTEGWDFLYSKYQFSLSSTEKSQIEFALCRTQNKEKLQWLLDESFKGDKIKTQEFPQILTLIGRNPVGYPLAWQFLRKNWNKLVQKFELGSSSIAHMVMGTTNQFSTRTRLEEVKGFFSSLKENGSQLRCVQQTIETIEENIGWMDKNFDKIRVWLQSEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1804
R free: 0.2133
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 289
Crystal growth procedure: 100 mM DL-malic acid, Bis-tris propane, pH 7.0, 25% PEG 1500
Matthews coefficient: 2.39
Solvent content (%): 48.45
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: 2019-04-10
Structure of MAP kinase phosphatase 5 in complex with 3,3-dimethyl-1-((5,6-dihydrobenzo[h]quinazolin-2-yl)thio)butan-2-one, an allosteric inhibitor (PDB entry 7UMU)
Macromolecule: Dual specificity protein phosphatase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 152 residues
Sequence: GSHMAELTPILPFLFLGNEQDAQDLDTMQRLNIGYVINVTTHLPLYHYEKGLFNYKRLPATDSNKQNLRQYFEEAFEFIEEAHQCGKGLLIHCQAGVSRSATIVIAYLMKHTRMTMTDAYKFVKGKRPIISPNLNFMGQLLEFEEDLNNGVT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.1973
R free: 0.2284
Average B factor: 49.49
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM HEPES (pH 7.5)
200 mM ammonium acetate
25% (w/v) PEG 3350
Matthews coefficient: 3.36
Solvent content (%): 63.34
Ligand: 1-[(benzo[h]quinazolin-2-yl)sulfanyl]-3,3-dimethylbutan-2-one (NUN)
Ligand formula: C18 H18 N2 O S
Ligand molecular weight: 310.413
Ligand SMILES: CC(C)(C)C(=O)CSc1ncc2ccc3ccccc3c2n1
Ligand InChI: InChI=1S/C18H18N2OS/c1-18(2,3)15(21)11-22-17-19-10-13-9-8-12-6-4-5-7-14(12)16(13)20-17/h4-10H,11H2,1-3H3
Release date: 2022-10-05
Crystal structure of TTK kinase domain in complex with compound 8 (PDB entry 7CHM)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 281 residues
Sequence: NECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2077
R free: 0.2531
Average B factor: 82.7
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 294.15
Crystal growth procedure: 7-9% PEG 10000, 0.08-0.14 M magnesium acetate, 0.1 M MES pH 6.0
Matthews coefficient: 3.33
Solvent content (%): 63.07
Ligand: 4-(cyclohexylamino)-2-[(2-methoxy-4-morpholin-4-ylcarbonyl-phenyl)amino]-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile (FZF)
Ligand formula: C25 H29 N7 O3
Ligand molecular weight: 475.543
Ligand SMILES: COc1cc(ccc1Nc2nc3c(c(c[nH]3)C#N)c(n2)NC4CCCCC4)C(=O)N5CCOCC5
Ligand InChI: InChI=1S/C25H29N7O3/c1-34-20-13-16(24(33)32-9-11-35-12-10-32)7-8-19(20)29-25-30-22-21(17(14-26)15-27-22)23(31-25)28-18-5-3-2-4-6-18/h7-8,13,15,18H,2-6,9-12H2,1H3,(H3,27,28,29,30,31)
Release date: 2021-05-12
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000148a (PDB entry 7GTT)
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): 1.93
R work: 0.2005
R free: 0.2371
Average B factor: 39.443
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.3
Solvent content (%): 62.7
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24