satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of small molecule beta-lactone 1 covalently bound to K-Ras(G12S) (PDB entry 7TLE)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 169 residues
Sequence: MTEYKLVVVGASGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98716752773
R work: 0.189088453173
R free: 0.233787340602
Average B factor: 29.5360900052
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M sodium acetate, 30% w/v PEG MME 2K, 0.2 M ammonium sulfate
Matthews coefficient: 2.33
Solvent content (%): 47.3
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2022-08-03
Crystal Structure of K-Ras(G12S) (PDB entry 7TLK)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 169 residues
Sequence: MTEYKLVVVGASGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71102224586
R work: 0.16906361931
R free: 0.205085961436
Average B factor: 16.3305950355
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris, 0.2 M CaCl2, 25% PEG 4K
Matthews coefficient: 2.16
Solvent content (%): 42.99
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2022-08-03
SYK Kinase domain in complex with diamine inhibitor 16 (PDB entry 6ZCY)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 299 residues
Sequence: MDTEVYESPYADPEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.188
R free: 0.223
Average B factor: 30.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 0.1M Na3Cit pH 6.4, 16% PEG3350, 0.2M KH2PO4
Matthews coefficient: 2.19
Solvent content (%): 43.88
Ligand: ~{N},1-dimethyl-5-[[4-[3-methyl-4-[[(3~{R})-pyrrolidin-3-yl]amino]pyrazol-1-yl]pyrimidin-2-yl]amino]indazole-3-carboxamide (QF8)
Ligand formula: C22 H26 N10 O
Ligand molecular weight: 446.508
Ligand SMILES: Cc1c(cn(n1)c2ccnc(n2)Nc3ccc4c(c3)c(nn4C)C(=O)NC)NC5CCNC5
Ligand InChI: InChI=1S/C22H26N10O/c1-13-17(26-15-6-8-24-11-15)12-32(29-13)19-7-9-25-22(28-19)27-14-4-5-18-16(10-14)20(21(33)23-2)30-31(18)3/h4-5,7,9-10,12,15,24,26H,6,8,11H2,1-3H3,(H,23,33)(H,25,27,28)/t15-/m1/s1
Release date: 2021-06-23
Human GAR transformylase in complex with GAR substrate and AGF320 inhibitor (PDB entry 8FJX)
Macromolecule: Trifunctional purine biosynthetic protein adenosine-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.4.13
Sequence length: 210 residues
Sequence: MARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.2027
R free: 0.2458
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris (pH 7.5), 0.333 mM NaCl, 20% polyethylene glycol (PEG) 4000, and 2% PEG 400
Matthews coefficient: 3.58
Solvent content (%): 65.69
Ligand: N-{5-[5-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)pentyl]thiophene-2-carbonyl}-L-glutamic acid (Y7L)
Ligand formula: C21 H25 N5 O6 S
Ligand molecular weight: 475.518
Ligand SMILES: c1cc(sc1CCCCCn2ccc3c2C(=O)NC(=N3)N)C(=O)NC(CCC(=O)O)C(=O)O
Ligand InChI: InChI=1S/C21H25N5O6S/c22-21-24-13-9-11-26(17(13)19(30)25-21)10-3-1-2-4-12-5-7-15(33-12)18(29)23-14(20(31)32)6-8-16(27)28/h5,7,9,11,14H,1-4,6,8,10H2,(H,23,29)(H,27,28)(H,31,32)(H3,22,24,25,30)/t14-/m0/s1
Release date: 2023-09-06
Ternary complex of DNA polymerase Mu (K438A/Q441A) with 1-nt gapped DNA (T:dGMPNPP) (PDB entry 7COC)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 482 residues
Sequence: MLPKRRRARVGSPSGDAASSTPPSTRFPGVAIYLVEPRMGRSRRAFLTGLARSKGFRVLDACSSEATHVVMEETSAEEAVSWQERRMAAAPPGCTPPALLDISWLTESLGAGQPVPVECRHRLEVAGPRKGPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSALFARELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1816
R free: 0.2115
Average B factor: 33.5882
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: Hexylene glycol, HEPES, PEG10000
Matthews coefficient: 1.93
Solvent content (%): 36.34
Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine (XG4)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc2c(n1C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-10-13-8-7(9(18)14-10)12-3-16(8)6-1-4(17)5(27-6)2-26-29(19,20)15-30(21,22)28-31(23,24)25/h3-6,17H,1-2H2,(H2,23,24,25)(H3,11,13,14,18)(H3,15,19,20,21,22)/t4-,5+,6+/m0/s1
Release date: 2021-06-30
Crystal structure of human C1s in complex with inhibitor gigastasin (PDB entry 5UBM)
Macromolecule: Complement C1s subcomponent
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.42
Sequence length: 252 residues
Sequence: RIIGGSDADIKNFPWQVFFDNPWAGGALINEYWVLTAAHVVEGNREPTMYVGSTSVQTSRLAKSKMLTPEHVFIHPGWKLLEVPEGRTNFDNDIALVRLKDPVKMGPTVSPICLPGTSSDYNLMDGDLGLISGWGRTEKRDRAVRLKAARLPVAPLRKCKEVKVEKPTADAEAYVFTPNMICAGGEKGMDSCKGDSGGAFAVQDPNDKTKFYAAGLVSWGPQCGTYGLYTRVKNYVDWIMKTMQENSTPRED
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1767
R free: 0.2223
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris, pH 5.5, 25 % PEG 3350
Matthews coefficient: 2.8
Solvent content (%): 56
Release date: 2017-11-08
Crystal Structure of BACE1 in complex with N-{3-[(4S,6S)-2-amino-4-methyl-6-(trifluoromethyl)-5,6-dihydro-4H-1,3-thiazin-4-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide (PDB entry 6JT4)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 416 residues
Sequence: GSHMLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1951
R free: 0.2339
Average B factor: 31.602
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.2 M sodium citrate tribasic pH 6.5, 0.2 M ammonium iodide, 20.5% w/v PEG 5000MME
Matthews coefficient: 2.73
Solvent content (%): 59.96
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: 2020-01-15
Crystal Structure of SETD2 Bound to an Indole-based Inhibitor (PDB entry 7TY2)
Macromolecule: Histone-lysine N-methyltransferase SETD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.359
Sequence length: 278 residues
Sequence: GETSVPPGSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKKNKSHRDIKRMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGKMKKERSRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.438
R work: 0.2126
R free: 0.27
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Potassium thiocyanate, 0.1 M HEPES 7.5, 18% w/v PEG 2000 MME
Matthews coefficient: 2.19
Solvent content (%): 43.85
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: 2022-08-31
Crystal structure of the bromodomain of human EP300 bound to the inhibitor XDM1 (PDB entry 5LPK)
Macromolecule: Histone acetyltransferase p300
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 122 residues
Sequence: APGQSKKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1764
R free: 0.2029
Average B factor: 41.958
Crystallization method: EVAPORATION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: PEG 3350, NaCl
Matthews coefficient: 2.71
Solvent content (%): 54.59
Ligand: ~{N}-[(3-chlorophenyl)methyl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole-2-carboxamide (XDM)
Ligand formula: C17 H19 Cl N2 O2
Ligand molecular weight: 318.798
Ligand SMILES: CCc1c(c([nH]c1C(=O)NCc2cccc(c2)Cl)C)C(=O)C
Ligand InChI: InChI=1S/C17H19ClN2O2/c1-4-14-15(11(3)21)10(2)20-16(14)17(22)19-9-12-6-5-7-13(18)8-12/h5-8,20H,4,9H2,1-3H3,(H,19,22)
Release date: 2017-08-16
CRYSTAL STRUCTURE OF FK1 DOMAIN OF FKBP52 IN COMPLEX WITH A BIO-INSPIRED HYBRID FLUORESCENT LIGAND (PDB entry 6RCY)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 148 residues
Sequence: MTAEEMKATESGAQSAPLPMEGVDISPKQDEGVLKVIKREGTGTEMPMIGDRVFVHYTGWLLDGTKFDSSLDRKDKFSFDLGKGEVIKAWDIAIATMKVGEVCHITCKPEYAYGSAGSPPKIPPNATLVFEVELFEFKGEDLTEEEDG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.218
R free: 0.244
Average B factor: 88.89
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.8M potassium phosphate, 0.8M sodium phosphate, 0.1M HEPES, pH 7.5
Matthews coefficient: 2.97
Solvent content (%): 58.55
Ligand: (2~{S})-5-carbamimidamido-2-[[(2~{S})-2-[[(2~{S})-1-[5-(dimethylamino)naphthalen-1-yl]sulfonylpiperidin-2-yl]carbonylamino]-4-phenyl-butanoyl]amino]pentanoic acid (K0T)
Ligand formula: C34 H45 N7 O6 S
Ligand molecular weight: 679.829
Ligand SMILES: CN(C)c1cccc2c1cccc2S(=O)(=O)N3CCCCC3C(=O)NC(CCc4ccccc4)C(=O)NC(CCCNC(=N)N)C(=O)O
Ligand InChI: InChI=1S/C34H45N7O6S/c1-40(2)28-17-8-14-25-24(28)13-9-18-30(25)48(46,47)41-22-7-6-16-29(41)32(43)38-26(20-19-23-11-4-3-5-12-23)31(42)39-27(33(44)45)15-10-21-37-34(35)36/h3-5,8-9,11-14,17-18,26-27,29H,6-7,10,15-16,19-22H2,1-2H3,(H,38,43)(H,39,42)(H,44,45)(H4,35,36,37)/t26-,27-,29-/m0/s1
Release date: 2020-05-13
Crystal structure of anaplastic lymphoma kinase (ALK) bound by Brigatinib (PDB entry 6MX8)
Macromolecule: ALK tyrosine kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 307 residues
Sequence: PNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1829
R free: 0.2271
Average B factor: 45.539
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M TRIS HCl pH 8.5, 19-27% PEG 3350, 2 mM TCEP
Matthews coefficient: 2.23
Solvent content (%): 44.87
Ligand: 5-chloro-N~4~-[2-(dimethylphosphoryl)phenyl]-N~2~-{2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl}pyrimidine-2,4-diamine (6GY)
Ligand formula: C29 H39 Cl N7 O2 P
Ligand molecular weight: 584.092
Ligand SMILES: CN1CCN(CC1)C2CCN(CC2)c3ccc(c(c3)OC)Nc4ncc(c(n4)Nc5ccccc5P(=O)(C)C)Cl
Ligand InChI: InChI=1S/C29H39ClN7O2P/c1-35-15-17-37(18-16-35)21-11-13-36(14-12-21)22-9-10-24(26(19-22)39-2)33-29-31-20-23(30)28(34-29)32-25-7-5-6-8-27(25)40(3,4)38/h5-10,19-21H,11-18H2,1-4H3,(H2,31,32,33,34)
Release date: 2018-12-12
SIRT1/Activator/Substrate Complex (PDB entry 4ZZJ)
Macromolecule: NAD-dependent protein deacetylase sirtuin-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 356 residues
Sequence: GPYTFVQQHLMIGTDPRTILKDLLPETIPPPELDDMTLWQIVINILSEPPKRKKRKDINTIEDAVKLLQECKKIIVLTGAGVSVSCGIPDFRSRDGIYARLAVDFPDLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRIIQCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPADEPLAIMKPEIVFFGENLPEQFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLCCNPVGGGSGGGSQYLFLPPNRYIFHGAEVYSDSEDDV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7403
R work: 0.1825
R free: 0.2214
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 5% v/v Tacsimate, pH .00.1 M HEPES pH 7.0 and 10% w/v PEG 5000 MME
Matthews coefficient: 4.85
Solvent content (%): 74.62
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: 2015-07-15
STRUCTURE OF THE CATALYTIC SUBUNIT OF PROTEIN KINASE CK2 (CK2ALPHA') IN COMPLEX WITH THE NON-HYDROLYZABLE ATP ANALOGUE AMPPNP (PDB entry 8QCG)
Macromolecule: Casein kinase II subunit alpha'
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: MGSSHHHHHHSQDPMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.04
R work: 0.1506
R free: 0.1703
Average B factor: 20.41
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 10 MIKROLITER CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WERE MIXED WITH 5 MIKROLITER RESERVOIR SOLUTION [810 MM LICL, 28% (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5]. AFTER EQUILIBRATION (SITTING DROP PLATES; VAPOUR DIFFUSION), CRYSTALLIZATION WAS INITIATED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING. THE ATP-ANALOGUE AMPPNP WAS COMBINED WITH THESE CRYSTALS BY SOAKING. A 20 MM AMPPNP SOLUTION IN 60 MM MGCL2 WAS PREPARED. FOR SOAKING, 3 MICROLITER OF THE CRYSTAL MOTHER LIQUOR WAS REMOVED AND REPLACED BY 3 MICROLITER OF 20 MM AMPPNP, 60 MM MGCL2. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.
Matthews coefficient: 2.19
Solvent content (%): 43.77
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2023-12-06
The LIMK1 Kinase Domain Bound To LIJTF500025 (PDB entry 7ATU)
Macromolecule: LIM domain kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 310 residues
Sequence: SMPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKVMRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASGMAYLHSMNIIHRDLNSHNCLVRENKNVVVADFGLARLMVDEKTQPEGLRSLKKPDRKKRYTVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFLDRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQLDRGFWETYRRGES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2401
R free: 0.3159
Average B factor: 59.79
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M citrate pH 5.9
0.2 M NaCl
8% jeffamine M-600
0.005 M iron chloride
Matthews coefficient: 2.43
Solvent content (%): 49.4
Ligand: (S)-2-benzyl-6-(8-chloro-5-methyl-4-oxo-2,3,4,5-tetrahydrobenzo[b][1,4]oxazepin-3-yl)-7-oxo-4,5,6,7-tetrahydro-2H-pyrazolo[3,4-c]pyridine-3-carboxamide (RXN)
Ligand formula: C24 H22 Cl N5 O4
Ligand molecular weight: 479.916
Ligand SMILES: CN1c2ccc(cc2OCC(C1=O)N3CCc4c(nn(c4C(=O)N)Cc5ccccc5)C3=O)Cl
Ligand InChI: InChI=1S/C24H22ClN5O4/c1-28-17-8-7-15(25)11-19(17)34-13-18(23(28)32)29-10-9-16-20(24(29)33)27-30(21(16)22(26)31)12-14-5-3-2-4-6-14/h2-8,11,18H,9-10,12-13H2,1H3,(H2,26,31)/t18-/m0/s1
Release date: 2020-12-23
Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to ACH000400 (PDB entry 8V42)
Macromolecule: Serine/threonine-protein kinase VRK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.199
R free: 0.231
Average B factor: 53.97
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 22% PEG3350, 20 mM Li2SO4, 0.1 M Buffer system SBG pH 7.0
Matthews coefficient: 2.56
Solvent content (%): 52.04
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2024-09-04
PanDDA analysis group deposition of ground-state model of human NUDT22 screened against the DSPL fragment library by X-ray Crystallography (PDB entry 5RKZ)
Macromolecule: Uridine diphosphate glucose pyrophosphatase NUDT22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.45
Sequence length: 304 residues
Sequence: SMDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPKFRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADPLGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVHELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLSGGPEAHESTGIFFVETQNVRRLPETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALLPPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.38
R work: 0.1833
R free: 0.2111
Average B factor: 21.45
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Matthews coefficient: 2.02
Solvent content (%): 39.07
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2020-07-22
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with alisertib (MLN8237) (PDB entry 5IA0)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.948
R work: 0.1937
R free: 0.2249
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 37.5 % MPD_P1k_P3350, 0.3 M Carboxylic Acids, 0.1 M BufferSystem3 pH 8.5
Matthews coefficient: 2.49
Solvent content (%): 50.68
Ligand: alisertib  (A5B)
Ligand formula: C27 H20 Cl F N4 O4
Ligand molecular weight: 518.924
Ligand SMILES: COc1cccc(c1C2=NCc3cnc(nc3-c4c2cc(cc4)Cl)Nc5ccc(c(c5)OC)C(=O)O)F
Ligand InChI: InChI=1S/C27H20ClFN4O4/c1-36-21-5-3-4-20(29)23(21)25-19-10-15(28)6-8-17(19)24-14(12-30-25)13-31-27(33-24)32-16-7-9-18(26(34)35)22(11-16)37-2/h3-11,13H,12H2,1-2H3,(H,34,35)(H,31,32,33)
Release date: 2016-11-09
Structure of human Parkin G319A (PDB entry 5C9V)
Macromolecule: E3 ubiquitin-protein ligase parkin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 330 residues
Sequence: GPAGRSIYNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYAAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAVFEASGTTTQAYRVDERAAEQARWEAASKETIKKTTKPCPRCHVPVEKNGGCMHMKCPQPQCRLEWCWNCGCEWNRVCMGDHWFDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1983
R free: 0.2287
Average B factor: 54.3
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 291
Crystal growth procedure: 1.8 M lithium sulphate, 0.01 M MgCl2, 0.05 M MES pH 5.6
Matthews coefficient: 3.63
Solvent content (%): 66.1
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: 2015-07-22