satarupa22/MacromolecularLigandDB huggingface dataset:
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_XST00000752b (PDB entry 5QFA)
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): 1.742
R work: 0.2019
R free: 0.2238
Average B factor: 40.2891
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: 3.39
Solvent content (%): 63.68
Ligand: [(4-chlorophenyl)sulfanyl]acetic acid (JNG)
Ligand formula: C8 H7 Cl O2 S
Ligand molecular weight: 202.658
Ligand SMILES: c1cc(ccc1SCC(=O)O)Cl
Ligand InChI: InChI=1S/C8H7ClO2S/c9-6-1-3-7(4-2-6)12-5-8(10)11/h1-4H,5H2,(H,10,11)
Release date: 2018-10-10
Crystal structure of human JMJD5 jmj-c domain (PDB entry 4QU1)
Macromolecule: Lysine-specific demethylase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.27
Sequence length: 236 residues
Sequence: GSTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1493
R free: 0.174
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES, pH 7.0, 8% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2.3
Solvent content (%): 46.45
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2015-07-15
LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (R)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N51) (PDB entry 6BH0)
Macromolecule: Lysine-specific demethylase 5A,  linked KDM5A JMJ domain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.985
R work: 0.1881
R free: 0.2187
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.23
Solvent content (%): 44.9
Ligand: 2-{(R)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (DO1)
Ligand formula: C22 H24 Cl N3 O3
Ligand molecular weight: 413.897
Ligand SMILES: c1ccc(c(c1)C(c2cc3c([nH]2)c(ccn3)C(=O)O)OCCN4CCCCC4)Cl
Ligand InChI: InChI=1S/C22H24ClN3O3/c23-17-7-3-2-6-15(17)21(29-13-12-26-10-4-1-5-11-26)19-14-18-20(25-19)16(22(27)28)8-9-24-18/h2-3,6-9,14,21,25H,1,4-5,10-13H2,(H,27,28)/t21-/m1/s1
Release date: 2018-03-28
PKG I's Carboyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with 8-Br-cGMP (PDB entry 5JAX)
Macromolecule: cGMP-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.12
Sequence length: 135 residues
Sequence: GSTGLIKHTEYMEFLKSVPTFQSLPEEILSKLADVLEETHYENGEYIIRQGARGDTFFIISKGTVNVTREDSPSEDPVFLRTLGKGDWFGEKALQGEDVRTANVIAAEAVTCLVIDRDSFKHLIGGLDDVSNKAY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.486
R work: 0.166
R free: 0.199
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 301
Crystal growth procedure: 30% PEG 400, 200 mM CaAc, 0.1M NaAc pH 4.5-4.8
Matthews coefficient: 1.94
Solvent content (%): 36.76
Ligand: 2-amino-8-bromo-9-[(2R,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-1,9-dihydro-6H-purin-6-one (6J7)
Ligand formula: C10 H11 Br N5 O7 P
Ligand molecular weight: 424.101
Ligand SMILES: C1C2C(C(C(O2)n3c4c(nc3Br)C(=O)NC(=N4)N)O)OP(=O)(O1)O
Ligand InChI: InChI=1S/C10H11BrN5O7P/c11-9-13-3-6(14-10(12)15-7(3)18)16(9)8-4(17)5-2(22-8)1-21-24(19,20)23-5/h2,4-5,8,17H,1H2,(H,19,20)(H3,12,14,15,18)/t2-,4-,5-,8-/m1/s1
Release date: 2017-04-19
PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-178-994 (PDB entry 5QQI)
Macromolecule: Ras-related C3 botulinum toxin substrate 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 178 residues
Sequence: SMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.2188
R free: 0.2767
Average B factor: 41.402
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1M bis-tris pH 5.5 24% PEG 3350
Matthews coefficient: 2.34
Solvent content (%): 47.5
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: 2019-12-18
Crystal structure of human acid ceramidase in covalent complex with carmofur (PDB entry 6MHM)
Macromolecule: Acid ceramidase subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.23
Sequence length: 131 residues
Sequence: DRHHHHHHKLQHAPPWTEDCRKSTYPPSGPTYRGAVPWYTINLDLPPYKRWHELMLDKAPMLKVIVNSLKNMINTFVPSGKVMQVVDEKLPGLLGNFPGPFEEEMKGIAAVTDIPLGEIISFNIFYELFTI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.743
R work: 0.2141
R free: 0.2616
Average B factor: 51.0869
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.3
Crystallization temperature (K): 298
Crystal growth procedure: 0.2 M sodium-phosphate-citrate, pH 4.3, 0.275 M lithium sulfate, and 18% polyethylene glycol 1000
Matthews coefficient: 2.66
Solvent content (%): 53.71
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: 2019-01-23
Structural Insights into Substrate and Inhibitor Binding Sites in Human Indoleamine 2,3-Dioxygenase 1 (PDB entry 5WMX)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 425 residues
Sequence: MSKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVGQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEGKGELNSKLEGKPIPNPLLGLDSTRTGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.69
R work: 0.21448
R free: 0.25415
Average B factor: 99.372
Crystallization method: MICROBATCH
Crystallization pH: 10
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Sodium thiosulfate, 100 mM pH 10.0 CAPS buffer, and 20% (w/v) PEG 8000
Matthews coefficient: 3.05
Solvent content (%): 59.68
Ligand: TRYPTOPHAN (TRP)
Ligand formula: C11 H12 N2 O2
Ligand molecular weight: 204.225
Ligand SMILES: c1ccc2c(c1)c(c[nH]2)CC(C(=O)O)N
Ligand InChI: InChI=1S/C11H12N2O2/c12-9(11(14)15)5-7-6-13-10-4-2-1-3-8(7)10/h1-4,6,9,13H,5,12H2,(H,14,15)/t9-/m0/s1
Release date: 2017-12-06
Structure of the Axl kinase domain in complex with a macrocyclic inhibitor (PDB entry 5U6B)
Macromolecule: Tyrosine-protein kinase receptor UFO
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 307 residues
Sequence: GSNSLGISEELKEKLRDVMVDRHKVALGKTLGEGEFGAVMEGQLNQDDSILKVAVKTMKIAICTRSELEDFLSEAVCMKEFDHPNVMRLIGVCFQGSERESFPAPVVILPFMKHGDLHSFLLYSRLGDQPVYLPTQMLVKFMADIASGMEYLSTKRFIHRDLAARNCMLNENMSVCVADFGLSKKIYNGDYYRQGRIAKMPVKWIAIESLADRVYTSKSDVWSFGVTMWEIATRGQTPYPGVENSEIYDYLRQGNRLKQPADCLDGLYALMSRCWELNPQDRPSFTELREDLENTLKALPPAQEPDE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.84
R work: 0.211
R free: 0.239
Average B factor: 56.98
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 1.2 microL of the protein-ligand complex (1:3 ratio of protein:ligand) and 1.2 microL of the reservoir solution (0.1 M Tris, pH 8.5, 0.2 M MgCl2, 30 % (w/v) PEG-4000, 1-2 % (v/v) 1-butanol).
Matthews coefficient: 2.41
Solvent content (%): 48.96
Ligand: (10R)-7-amino-11-chloro-12-fluoro-1-(2-hydroxyethyl)-3,10,16-trimethyl-16,17-dihydro-1H-8,4-(azeno)pyrazolo[4,3-h][2,5,11]benzoxadiazacyclotetradecin-15(10H)-one (7YS)
Ligand formula: C21 H22 Cl F N6 O3
Ligand molecular weight: 460.889
Ligand SMILES: Cc1c-2c(n(n1)CCO)CN(C(=O)c3ccc(c(c3C(Oc4c(ncc2n4)N)C)Cl)F)C
Ligand InChI: InChI=1S/C21H22ClFN6O3/c1-10-16-14-8-25-19(24)20(26-14)32-11(2)17-12(4-5-13(23)18(17)22)21(31)28(3)9-15(16)29(27-10)6-7-30/h4-5,8,11,30H,6-7,9H2,1-3H3,(H2,24,25)/t11-/m1/s1
Release date: 2017-07-26
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B23 (PDB entry 7TH7)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 163 residues
Sequence: NPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.135
R free: 0.1473
Average B factor: 12.77
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.2
Crystallization temperature (K): 298
Crystal growth procedure: 21% PEG 3350
0.5 M KH2PO4
Protein and inhibitor were mixed in ratio 1:3
1 uL of protein:inhibitor complex was mixed with 1 uL mother liquor
Matthews coefficient: 2.47
Solvent content (%): 51.59
Ligand: 3-(4'-{[(4S,7S,11R,19S)-19-{[2-(2-aminoethoxy)ethyl]carbamoyl}-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,13,14,15,16,17,18,19,20,21,22-icosahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosin-4-yl]methyl}[1,1'-biphenyl]-4-yl)propanoic acid (I5E)
Ligand formula: C52 H63 N7 O9
Ligand molecular weight: 930.098
Ligand SMILES: c1ccc(cc1)CC23CCCN(C2)C(=O)CCC(=O)NCCC(NC(=O)Cc4ccccc4CNC(=O)C(NC3=O)Cc5ccc(cc5)c6ccc(cc6)CCC(=O)O)C(=O)NCCOCCN
Ligand InChI: InChI=1S/C52H63N7O9/c53-25-29-68-30-27-55-49(65)43-23-26-54-45(60)20-21-47(62)59-28-6-24-52(35-59,33-38-7-2-1-3-8-38)51(67)58-44(50(66)56-34-42-10-5-4-9-41(42)32-46(61)57-43)31-37-13-18-40(19-14-37)39-16-11-36(12-17-39)15-22-48(63)64/h1-5,7-14,16-19,43-44H,6,15,20-35,53H2,(H,54,60)(H,55,65)(H,56,66)(H,57,61)(H,58,67)(H,63,64)/t43-,44-,52-/m0/s1
Release date: 2022-08-24
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with dATP (PDB entry 6CR4)
Macromolecule: Template Strand
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 16 residues
Sequence: CCGACTGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.173
R free: 0.2135
Average B factor: 21.8704
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.3
Solvent content (%): 46.54
Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTP)
Ligand formula: C10 H16 N5 O12 P3
Ligand molecular weight: 491.182
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
Release date: 2018-07-18
Co-crystal structure of LMW-PTP in complex with MES (PDB entry 5KQM)
Macromolecule: Low molecular weight phosphotyrosine protein phosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 178 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMAEQATKSVLFVCLGNICRSPIAEAVFRKLVTDQNISENWRVDSAATSGYEIGNPPDYRGQSCMKRHGIPMSHVARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSDFETVYQQCVRCCRAFLEKAH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.1847
R free: 0.2281
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEGME 5000, 0.2 M ammonium sulfate, 100 mM MES, pH=6.5
Matthews coefficient: 2.17
Solvent content (%): 43.37
Ligand: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID (MES)
Ligand formula: C6 H13 N O4 S
Ligand molecular weight: 195.237
Ligand SMILES: C1COCC[NH+]1CCS(=O)(=O)[O-]
Ligand InChI: InChI=1S/C6H13NO4S/c8-12(9,10)6-3-7-1-4-11-5-2-7/h1-6H2,(H,8,9,10)
Release date: 2016-10-12
Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives (PDB entry 5LT8)
Macromolecule: Histone-lysine N-methyltransferase SETD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 295 residues
Sequence: MHHHHHHSSGRENLYFQGETSVPPGSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKKNKSHRDIKRMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGKMKKERSRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.17425
R free: 0.21551
Average B factor: 30.766
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M HEPES, PH7.3, 0.1MKSCN, 25-30%MPEG2000
Matthews coefficient: 1.87
Solvent content (%): 34.28
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: 2016-10-05
Crystal Structure of human cyclic GMP-AMP synthase in complex with 5-bromo-2-hydroxy-N-[[3-(1-methylpyrazol-4-yl)phenyl]methyl]benzamide (PDB entry 7FTW)
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): 2.208
R work: 0.2116
R free: 0.2608
Average B factor: 84.9179
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: 2.57
Solvent content (%): 52.09
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: 2024-02-21
Crystal Structure of c-Cbl TKBD in complex with SPRY2 peptide (54-60, pY55) Refined to 2.2A Resolution (PDB entry 5HL0)
Macromolecule: E3 ubiquitin-protein ligase CBL
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 308 residues
Sequence: SNAPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRNQNPDLTG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1902
R free: 0.2366
Average B factor: 45.8552
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 16% (w/v) PEG 8000, 0.04M Potassium phosphate (monobasic), 20% (v/v) glycerol
Matthews coefficient: 3.4
Solvent content (%): 63.8
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-01-18
LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(1-methyl-1H-imidazol-2-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N47) (PDB entry 6BGZ)
Macromolecule: Lysine-specific demethylase 5A, linked KDM5A JMJ domain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.688
R work: 0.1865
R free: 0.197
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.24
Solvent content (%): 45.1
Ligand: 2-{(S)-(2-chlorophenyl)[2-(1-methyl-1H-imidazol-2-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (DNV)
Ligand formula: C21 H19 Cl N4 O3
Ligand molecular weight: 410.854
Ligand SMILES: Cn1ccnc1CCOC(c2ccccc2Cl)c3cc4c([nH]3)c(ccn4)C(=O)O
Ligand InChI: InChI=1S/C21H19ClN4O3/c1-26-10-9-24-18(26)7-11-29-20(13-4-2-3-5-15(13)22)17-12-16-19(25-17)14(21(27)28)6-8-23-16/h2-6,8-10,12,20,25H,7,11H2,1H3,(H,27,28)/t20-/m0/s1
Release date: 2018-03-28
Crystal structure of JAK2 JH1 in complex with gandotinib (PDB entry 8BM2)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 317 residues
Sequence: MGHHHHHHSSGVDLGTENLYFQSMDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1773
R free: 0.2021
Average B factor: 26.34
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.2
Crystallization temperature (K): 295
Crystal growth procedure: 1.7 M Na-malonate, 0.1 M Gly-Gly pH 8.2
Matthews coefficient: 2.53
Solvent content (%): 51.31
Ligand: 3-[(4-chloranyl-2-fluoranyl-phenyl)methyl]-2-methyl-~{N}-(5-methyl-1~{H}-pyrazol-3-yl)-8-(morpholin-4-ylmethyl)imidazo[1,2-b]pyridazin-6-amine (QQC)
Ligand formula: C23 H25 Cl F N7 O
Ligand molecular weight: 469.942
Ligand SMILES: Cc1cc(n[nH]1)Nc2cc(c3nc(c(n3n2)Cc4ccc(cc4F)Cl)C)CN5CCOCC5
Ligand InChI: InChI=1S/C23H25ClFN7O/c1-14-9-21(29-28-14)27-22-11-17(13-31-5-7-33-8-6-31)23-26-15(2)20(32(23)30-22)10-16-3-4-18(24)12-19(16)25/h3-4,9,11-12H,5-8,10,13H2,1-2H3,(H2,27,28,29,30)
Release date: 2023-11-22
Crystal structure of ALPK-1 N-terminal domain in complex with ADP-heptose (PDB entry 5Z2C)
Macromolecule: Alpha-protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11
Sequence length: 446 residues
Sequence: MNNQKVVAVLLQECKQVLDQLLLEAPDVSEEDKSEDQRCRALLPSELRTLIQEAKEMKWPFVPEKWQYKQAVGPEDKTNLKDVIGAGLQQLLASLRASILARDCAAAAAIVFLVDRFLYGLDVSGKLLQVAKGLHKLQPATPIAPQVVIRQARISVNSGKLLKAEYILSSLISNNGATGTWLYRNESDKVLVQSVCIQIRGQILQKLGMWYEAAELIWASIVGYLALPQPDKKGLSTSLGILADIFVSMSKNDYEKFKNNPQINLSLLKEFDHHLLSAAEACKLAAAFSAYTPLFVLTAVNIRGTCLLSYSSSNDCPPELKNLHLCEAKEAFEIGLLTKRDDEPVTGKQELHSFVKAAFGLTTVHRRLHGETGTVHAASQLCKEAMGKLYNFSTSSRSQDREALSQEVMSVIAQVKEHLQVQSFSNVDDRSYVPESFECRLDKLIL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.594
R work: 0.242
R free: 0.2628
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4
Crystallization temperature (K): 293
Crystal growth procedure: 1.4M sodium formate, 0.1M sodium acetate
Matthews coefficient: 3.3
Solvent content (%): 62.76
Ligand: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4S,5S,6R)-6-[(1S)-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate (AYU)
Ligand formula: C17 H27 N5 O16 P2
Ligand molecular weight: 619.368
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)C(CO)O)O)O)O)O)O)N
Ligand InChI: InChI=1S/C17H27N5O16P2/c18-14-7-15(20-3-19-14)22(4-21-7)16-11(28)8(25)6(35-16)2-34-39(30,31)38-40(32,33)37-17-12(29)9(26)10(27)13(36-17)5(24)1-23/h3-6,8-13,16-17,23-29H,1-2H2,(H,30,31)(H,32,33)(H2,18,19,20)/t5-,6+,8+,9-,10-,11+,12-,13+,16+,17-/m0/s1
Release date: 2018-08-22