satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of ULK1 bound to a potent inhibitor (PDB entry 4WNP)
Macromolecule: Serine/threonine-protein kinase ULK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 287 residues
Sequence: GGGSMEPGRGGTETVGKFEFSRKDLIGHGAFAVVFKGRHRAAHDLEVAVKCINKKNLAKSQTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAATLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKTLVPTIPRETSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDASPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.1922
R free: 0.2264
Average B factor: 43.4051
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 1.55 M sodium malonate pH 7.0,  0.35 M sodium malonate pH 5.0
Matthews coefficient: 2.22
Solvent content (%): 44.68
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: 2015-01-14
Crystal structure of TrkA kinase with repotrectinib (PDB entry 7VKO)
Macromolecule: Tyrosine-protein kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 326 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQGAMGSGIRVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.18412
R free: 0.26738
Average B factor: 95.454
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M citric acid PH 5.0, 8M ammonium sulfate
Matthews coefficient: 2.9
Solvent content (%): 57.59
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: 2021-10-13
DNA Polymerase Mu Product Complex, 10 mM Mg2+ (270 min) (PDB entry 5TYF)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.971
R work: 0.1737
R free: 0.205
Average B factor: 30.9667
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.68
Solvent content (%): 54.05
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: 2017-08-30
LIM domain kinase 2 (LIMK2) in complex with TH-470 (PDB entry 7QHG)
Macromolecule: LIM domain kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 305 residues
Sequence: SMDLIHGEVLGKGFFGQAIKVTHKATGKVMVMKELIRCDEETQKTFLTEVKVMRSLDHPNVLKFIGVLYKDKKLNLLTEYIEGGTLKDFLRSMDPFPWQQKVRFAKGIASGMAYLHSMCIIHRDLNSHNCLIKLDKTVVVADFGLSRLIVEERKRAPMEKATTKKRTLRKNDRKKRYTVVGNPYWMAPEMLNGKSYDETVDIFSFGIVLCEIIGQVYADPDCLPRTLDFGLNVKLFWEKFVPTDCPPAFFPLAAICCRLEPESRPAFSKLEDSFEALSLYLGELGIPLPAELEELDHTVSMQYGL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1652
R free: 0.177
Average B factor: 20.83
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M bis-tris-propane pH 7.5, 
0.2 M Na2SO4, 
10% ethylene glycol, 
17% PEG3.35K
Matthews coefficient: 2.48
Solvent content (%): 50.38
Ligand: 2-(2-methylpropanoylamino)-~{N}-[2-[(phenylmethyl)-[4-(phenylsulfamoyl)phenyl]carbonyl-amino]ethyl]-1,3-thiazole-5-carboxamide (T3B)
Ligand formula: C30 H31 N5 O5 S2
Ligand molecular weight: 605.728
Ligand SMILES: CC(C)C(=O)Nc1ncc(s1)C(=O)NCCN(Cc2ccccc2)C(=O)c3ccc(cc3)S(=O)(=O)Nc4ccccc4
Ligand InChI: InChI=1S/C30H31N5O5S2/c1-21(2)27(36)33-30-32-19-26(41-30)28(37)31-17-18-35(20-22-9-5-3-6-10-22)29(38)23-13-15-25(16-14-23)42(39,40)34-24-11-7-4-8-12-24/h3-16,19,21,34H,17-18,20H2,1-2H3,(H,31,37)(H,32,33,36)
Release date: 2021-12-22
Crystal structure of human CPSF73 catalytic segment in complex with compound 2 (PDB entry 8T1R)
Macromolecule: Cleavage and polyadenylation specificity factor subunit 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27
Sequence length: 479 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMSAIPAEESDQLLIRPLGAGQEVGRSCIILEFKGRKIMLDCGIHPGLEGMDALPYIDLIDPAEIDLLLISHFHLDHCGALPWFLQKTSFKGRTFMTHATKAIYRWLLSDYVKVSNISADDMLYTETDLEESMDKIETINFHEVKEVAGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPNIKPDILIIESTYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPVFALGRAQELLLILDEYWQNHPELHDIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQININNPFVFKHISNLKSMDHFDDIGPSVVMASPGMMQSGLSRELFESWCTDKRNGVIIAGYCVEGTLAKHIMSEPEEITTMSGQKLPLKMSVDYISFSAHTDYQQTSEFIRALKPPHVILVHGEQNEMARLKAALIREYEDNDEVHIEVHNPRNTEAVTLNFR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.196
R free: 0.2499
Average B factor: 51.93
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 18-30% (w/v) PEG3350, 200-250 mM ammonium sulfate and 0.1 M Bis-Tris pH 6.3-6.7
Matthews coefficient: 2.28
Solvent content (%): 46.13
Ligand: 3-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-5-yl]-~{N}-[3-(3-methoxyphenyl)phenyl]propanamide (XZC)
Ligand formula: C23 H23 B N O5
Ligand molecular weight: 404.243
Ligand SMILES: [B-]1(c2c(cccc2CCC(=O)Nc3cccc(c3)c4cccc(c4)OC)CO1)(O)O
Ligand InChI: InChI=1S/C23H23BNO5/c1-29-21-10-4-7-18(14-21)17-6-3-9-20(13-17)25-22(26)12-11-16-5-2-8-19-15-30-24(27,28)23(16)19/h2-10,13-14,27-28H,11-12,15H2,1H3,(H,25,26)/q-1
Release date: 2023-11-08
Crystal structure of DNA polymerase alpha catalytic core in complex with dCTP and template/primer having T-C mismatch at the post-insertion site (PDB entry 7N2M)
Macromolecule: DNA polymerase alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 922 residues
Sequence: DEEQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTLYFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEKNYAFEIPDVPEKSEYLEVKYSAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKSPQLLNQPVSWCKAEAMALKPDLVNVIKDVSPPPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFCVVSKPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGGRSGFGERNATCGRMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIFRKPQQKLGDEDEEIDGDTNKYKKGRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVASEAQKVTEDGEQEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDAVLIATWLGLDPTQFRVHHYHKDEEN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.195
R free: 0.228
Average B factor: 51.1
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.8 mM zinc sulfate, 8.8% v/v PEG MME 550, and 50 mM MES pH 6.5
Matthews coefficient: 4.52
Solvent content (%): 72.81
Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
Release date: 2022-04-20
histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2BK120 (PDB entry 6ACO)
Macromolecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 270 residues
Sequence: SARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.16096
R free: 0.217
Average B factor: 29.941
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate (pH 6.5), 30%(w/v) PEG8000
Matthews coefficient: 2.01
Solvent content (%): 38.78
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: 2019-07-24
Human DNA Pol eta S113A with rA-ended primer and dAMPNPP (PDB entry 7M7R)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERAAIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.183
R free: 0.2209
Average B factor: 21.3475
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: 15% PEG 2000 MME,
100 mM MES
Matthews coefficient: 2.1
Solvent content (%): 41.3
Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine (DZ4)
Ligand formula: C10 H17 N6 O11 P3
Ligand molecular weight: 490.197
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O11P3/c11-9-8-10(13-3-12-9)16(4-14-8)7-1-5(17)6(26-7)2-25-28(18,19)15-29(20,21)27-30(22,23)24/h3-7,17H,1-2H2,(H2,11,12,13)(H2,22,23,24)(H3,15,18,19,20,21)/t5-,6+,7+/m0/s1
Release date: 2021-06-02
Crystal structure of GSK3b in complex with Compound 15: 2-[(cyclopropylcarbonyl)amino]-N-(4-methoxypyridin-3-yl)pyridine-4-carboxamide (PDB entry 5F94)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 350 residues
Sequence: KVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARIQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.1887
R free: 0.2257
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 298
Crystal growth procedure: Crystals grown in the presence of 25% PEG 1500 and 0.1 M MMT pH 4.0
Matthews coefficient: 3.83
Solvent content (%): 67.87
Ligand: 2-[(cyclopropylcarbonyl)amino]-N-(4-methoxypyridin-3-yl)pyridine-4-carboxamide (3UO)
Ligand formula: C16 H16 N4 O3
Ligand molecular weight: 312.323
Ligand SMILES: COc1ccncc1NC(=O)c2ccnc(c2)NC(=O)C3CC3
Ligand InChI: InChI=1S/C16H16N4O3/c1-23-13-5-6-17-9-12(13)19-16(22)11-4-7-18-14(8-11)20-15(21)10-2-3-10/h4-10H,2-3H2,1H3,(H,19,22)(H,18,20,21)
Release date: 2016-02-03
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMSOA000953b (PDB entry 5QFX)
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): 1.824
R work: 0.2026
R free: 0.2215
Average B factor: 48.1265
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: 3.3
Solvent content (%): 62.7
Ligand: 4-phenoxybenzoic acid (JO4)
Ligand formula: C13 H10 O3
Ligand molecular weight: 214.217
Ligand SMILES: c1ccc(cc1)Oc2ccc(cc2)C(=O)O
Ligand InChI: InChI=1S/C13H10O3/c14-13(15)10-6-8-12(9-7-10)16-11-4-2-1-3-5-11/h1-9H,(H,14,15)
Release date: 2018-10-10
Carbonic Anhydrase IX like mutant in Complex with Steriod_Sulphamoyl inhibitor VK42 (PDB entry 8OKT)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTARYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.15729
R free: 0.17752
Average B factor: 15.54
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-H2SO4
Matthews coefficient: 2.05
Solvent content (%): 40.09
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: 2024-04-10
Crystal structure of human Caspase-1 with N-{3-[1-((S)-2-Hydroxy-5-oxo-tetrahydro-furan-3-ylcarbamoyl)-ethyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydro-pyrimidin-5-yl}-4-(quinoxalin-2-ylamino)-benzamide (PDB entry 6F6R)
Macromolecule: Caspase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.36
Sequence length: 180 residues
Sequence: QDNPAMPTSSGSEGNVKLCSLEEAQRIWKQKSAEIYPIMDKSSRTRLALIICNEEFDSIPRRTGAEVDITGMTMLLQNLGYSVDVKKNLTASDMTTELEAFAHRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQLNAIFNMLNTKNCPSLKDKPKVIIIQACRGDSPGVVWFKD
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.173
R free: 0.205
Average B factor: 41.04
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES (pH7.4), 2 M (NH4)2SO4 and 25 mM DTT
Matthews coefficient: 4.63
Solvent content (%): 73.43
Ligand: (3~{S})-3-[[(2~{R})-2-[3-methyl-2,6-bis(oxidanylidene)-5-[[4-(quinoxalin-2-ylamino)phenyl]carbonylamino]pyrimidin-1-yl]propanoyl]amino]-4-oxidanyl-butanoic acid (CVE)
Ligand formula: C27 H27 N7 O7
Ligand molecular weight: 561.546
Ligand SMILES: CC(C(=O)NC(CC(=O)O)CO)N1C(=O)C(=CN(C1=O)C)NC(=O)c2ccc(cc2)Nc3cnc4ccccc4n3
Ligand InChI: InChI=1S/C27H27N7O7/c1-15(24(38)30-18(14-35)11-23(36)37)34-26(40)21(13-33(2)27(34)41)32-25(39)16-7-9-17(10-8-16)29-22-12-28-19-5-3-4-6-20(19)31-22/h3-10,12-13,15,18,35H,11,14H2,1-2H3,(H,29,31)(H,30,38)(H,32,39)(H,36,37)/t15-,18+/m1/s1
Release date: 2018-05-02
Crystal structure of ZAK in complex with compound D2829 (PDB entry 5X5O)
Macromolecule: Mitogen-activated protein kinase kinase kinase MLT
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 310 residues
Sequence: GAMGSGASFVQIKFDDLQFFENCGGGSFGSVYRAKWISQDKEVAVKKLLKIEKEAEILSVLSHRNIIQFYGVILEPPNYGIVTEYASLGSLYDYINSNRSEEMDMDHIMTWATDVAKGMHYLHMEAPVKVIHRDLKSRNVVIAADGVLKICDFGASRFHNHTTHMSLVGTFPWMAPEVIQSLPVSETCDTYSYGVVLWEMLTREVPFKGLEGLQVAWLVVEKNERLTIPSSCPRSFAELLHQCWEADAKKRPSFKQIISILESMSNDTSLPDKCNSFLHNKAEWRCEIEATLERLKKLERDLSFKEQELK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.868
R work: 0.1898
R free: 0.2264
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Trimethylamine N-oxide dehydrate, 0.1 M Tris, 20% w/v Polyethylene glycol monomethyl ether 2000, pH8.5
Matthews coefficient: 1.85
Solvent content (%): 33.42
Ligand: N-[2,4-bis(fluoranyl)-3-[2-(3-methoxy-1H-pyrazolo[3,4-b]pyridin-5-yl)ethynyl]phenyl]-3-bromanyl-benzenesulfonamide (7Z0)
Ligand formula: C21 H13 Br F2 N4 O3 S
Ligand molecular weight: 519.319
Ligand SMILES: COc1c2cc(cnc2[nH]n1)C#Cc3c(ccc(c3F)NS(=O)(=O)c4cccc(c4)Br)F
Ligand InChI: InChI=1S/C21H13BrF2N4O3S/c1-31-21-16-9-12(11-25-20(16)26-27-21)5-6-15-17(23)7-8-18(19(15)24)28-32(29,30)14-4-2-3-13(22)10-14/h2-4,7-11,28H,1H3,(H,25,26,27)
Release date: 2017-12-27
CRYSTAL STRUCTURE OF BTK with CNX 774 (PDB entry 5P9K)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 279 residues
Sequence: GKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.28
R work: 0.18
R free: 0.1946
Average B factor: 19.5302
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: PEG 3350, sodium actate, BisTrisPropane
Matthews coefficient: 2.2
Solvent content (%): 44.14
Ligand: 4-[4-[[5-fluoranyl-4-[[3-(propanoylamino)phenyl]amino]pyrimidin-2-yl]amino]phenoxy]-~{N}-methyl-pyridine-2-carboxamide (7G8)
Ligand formula: C26 H24 F N7 O3
Ligand molecular weight: 501.512
Ligand SMILES: CCC(=O)Nc1cccc(c1)Nc2c(cnc(n2)Nc3ccc(cc3)Oc4ccnc(c4)C(=O)NC)F
Ligand InChI: InChI=1S/C26H24FN7O3/c1-3-23(35)31-17-5-4-6-18(13-17)32-24-21(27)15-30-26(34-24)33-16-7-9-19(10-8-16)37-20-11-12-29-22(14-20)25(36)28-2/h4-15H,3H2,1-2H3,(H,28,36)(H,31,35)(H2,30,32,33,34)
Release date: 2017-05-24
Crystal structure of Akt1 (aa 123-480) kinase with a bisubstrate (PDB entry 6NPZ)
Macromolecule: RAC-alpha serine/threonine-protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 358 residues
Sequence: GSPSDNSGAEEMEVSLAKPKHRVTMNEFEYLKLLGKGTFGKVILVKEKATGRYYAMKILKKEVIVAKDEVAHTLTENRVLQNSRHPFLTALKYSFQTHDRLCFVMEYANGGELFFHLSRERVFSEDRARFYGAEIVSALDYLHSEKNVVYRDLKLENLMLDKDGHIKITDFGLCKEGIKDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILMEEIRFPRTLGPEAKSLLSGLLKKDPKQRLGGGSEDAKEIMQHRFFAGIVWQHVYEKKLSPPFKPQVTSETDTRYFDEEFTAQMITITPPDQDDSMECVDSERRPHFPQFSYSASGTA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.1853
R free: 0.241
Average B factor: 39.787
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 12.5% PEG3350, 0.1 M HEPES-HCl, 0.2 M ammonium acetate
Matthews coefficient: 2.5
Solvent content (%): 50.87
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: 2019-01-30
HRAS R97F Crystal Form 2 (PDB entry 8ELR)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 189 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYFEQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.188
R free: 0.244
Average B factor: 34.1893
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: Calcium Acetate
PEG3350,
Magnesium Chloride,
HEPES,
Sodium Chloride,
DTT
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2023-09-06
Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487 (PDB entry 6RLW)
Macromolecule: N-glycosylase/DNA lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 337 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADLRQSR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2225
R free: 0.2741
Average B factor: 41.301
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 294
Crystal growth procedure: 0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 48 % v/v Precipitant Mix from 4 Morpheus screen (Molecular Dimensions)
Matthews coefficient: 2.3
Solvent content (%): 46.7
Ligand: 4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide (K8Q)
Ligand formula: C19 H18 Br I N4 O2
Ligand molecular weight: 541.18
Ligand SMILES: c1cc2c(c(c1)Br)NC(=O)N2C3CCN(CC3)C(=O)Nc4ccc(cc4)I
Ligand InChI: InChI=1S/C19H18BrIN4O2/c20-15-2-1-3-16-17(15)23-19(27)25(16)14-8-10-24(11-9-14)18(26)22-13-6-4-12(21)5-7-13/h1-7,14H,8-11H2,(H,22,26)(H,23,27)
Release date: 2020-07-22
CRYSTAL STRUCTURE OF YVAD-CMK BOUND HUMAN LEGUMAIN (AEP) IN COMPLEX WITH COMPOUND 11B (PDB entry 5LU8)
Macromolecule: AC-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONE
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 6 residues
Sequence: XYVADX
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.219
R free: 0.251
Average B factor: 32.4
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES PH 7.5, 0.2 M LITHIUM
 SULFATE MONOHYDRATE, 25 % PEG 3350, VAPOR DIFFUSION, SITTING
 DROP, TEMPERATURE 293K
Matthews coefficient: 2.66
Solvent content (%): 53.84
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2017-03-29