satarupa22/MacromolecularLigandDB huggingface dataset:
BTK kinase domain with inhibitor 1 (PDB entry 5FBN)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 271 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.17945
R free: 0.22596
Average B factor: 23.103
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 20% v/v PEG 20000 0.1M NaCl 0.1M Na MES pH 6.5 2.5 mM mM (S)-4-(8-amino-3-(1-(4-(dimethylamino)butanoyl)pyrrolidin-2-yl)imidazo[1,5-a]pyrazin-1-yl)-N-(thiazol-2-yl)benzamide 5.0 mM (R)-4-(8-amino-3-(1-(3-methyloxetane-3-carbonyl)piperidin-3-yl)imidazo[1,5-a]pyrazin-1-yl)-N-(4-(trifluoromethyl)pyridin-2-yl)benzamide
Matthews coefficient: 2.23
Solvent content (%): 44.83
Ligand: 4-[8-azanyl-3-[(3~{R})-1-(3-methyloxetan-3-yl)carbonylpiperidin-3-yl]imidazo[1,5-a]pyrazin-1-yl]-~{N}-[4-(trifluoromethyl)pyridin-2-yl]benzamide (5WF)
Ligand formula: C29 H28 F3 N7 O3
Ligand molecular weight: 579.573
Ligand SMILES: CC1(COC1)C(=O)N2CCCC(C2)c3nc(c4n3ccnc4N)c5ccc(cc5)C(=O)Nc6cc(ccn6)C(F)(F)F
Ligand InChI: InChI=1S/C29H28F3N7O3/c1-28(15-42-16-28)27(41)38-11-2-3-19(14-38)25-37-22(23-24(33)35-10-12-39(23)25)17-4-6-18(7-5-17)26(40)36-21-13-20(8-9-34-21)29(30,31)32/h4-10,12-13,19H,2-3,11,14-16H2,1H3,(H2,33,35)(H,34,36,40)/t19-/m1/s1
Release date: 2016-02-03
Crystal structure of human MTH1(G2K mutant) in complex with 8-oxo-dGTP at pH 8.6 (PDB entry 8I1A)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 156 residues
Sequence: MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1501
R free: 0.1916
Average B factor: 17.77
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: sodium citrate, tris, NaCl
Matthews coefficient: 1.89
Solvent content (%): 34.98
Ligand: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (8DG)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(27-5)2-26-31(22,23)29-32(24,25)28-30(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
Release date: 2023-03-22
Carbonic anhydrase II in complex with 4-(3-quinolinyl)-benzenesulfonamide (PDB entry 5SZ3)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.689
R work: 0.1633
R free: 0.2031
Average B factor: 18.2427
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.6M Sodium Citrate, 50mM Tris pH 7.8
Matthews coefficient: 2.11
Solvent content (%): 41.64
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: 2016-12-21
Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with compound 2 (AA-CS-9-003) (PDB entry 8BGC)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 338 residues
Sequence: SMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2225
R free: 0.2534
Average B factor: 58.28
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350
Matthews coefficient: 3.16
Solvent content (%): 61.07
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: 2022-11-23
Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate chelating water-soluble inhibitor (DC24). (PDB entry 5I2Z)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 159 residues
Sequence: MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.214
R free: 0.263
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: Protein-ligand:  hMMP12 F67D E219Q at 465 micro-M, 20 milli-M  acetohydroxamic acid in 0.020M Tris-HCl, 3 milli-M CaCl2, 0.2M NaCl, pH 7.5, 0.2 milli-M inhibitor (DC24) 10% DMSO
Precipitant: 35% PEG4K, 0.2M imidazole piperidine, 15% dioxane, pH 8.5.
Cryoprotectant: 
40% cryomix: (25 % diethylene glycol + 12.5 % glycerol + 25 % 1,2-propanediol + 12.5 % 1,4-dioxane) 25% PEG 6K, 100mM TRIS HCl, pH 8.0
Matthews coefficient: 2.8
Solvent content (%): 56.02
Ligand: N-[([1,1'-biphenyl]-4-yl)sulfonyl]-N-({1-[3,4,6-tri-O-acetyl-2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1H-1,2,3-triazol-4-yl}methyl)-D-valine (V24)
Ligand formula: C34 H41 N5 O12 S
Ligand molecular weight: 743.781
Ligand SMILES: CC(C)C(C(=O)O)N(Cc1cn(nn1)C2C(C(C(C(O2)COC(=O)C)OC(=O)C)OC(=O)C)NC(=O)C)S(=O)(=O)c3ccc(cc3)c4ccccc4
Ligand InChI: InChI=1S/C34H41N5O12S/c1-19(2)30(34(44)45)39(52(46,47)27-14-12-25(13-15-27)24-10-8-7-9-11-24)17-26-16-38(37-36-26)33-29(35-20(3)40)32(50-23(6)43)31(49-22(5)42)28(51-33)18-48-21(4)41/h7-16,19,28-33H,17-18H2,1-6H3,(H,35,40)(H,44,45)/t28-,29-,30-,31-,32-,33-/m1/s1
Release date: 2016-07-06
plasminogen binding group A streptococcal M protein (PDB entry 6OG4)
Macromolecule: Plasminogen
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.7
Sequence length: 87 residues
Sequence: AAQPAEECMHASGENYDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNPDRELRPWCFTTDPNKRWELCDIPRCTT
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2029
R free: 0.2203
Average B factor: 32.39
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, pH 7.0, 2 M ammonium sulfate
Matthews coefficient: 2.36
Solvent content (%): 47.84
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: 2019-07-24
Crystal structure of the CREBBP bromodomain in complex with a benzo-diazepine ligand (PDB entry 6YIJ)
Macromolecule: CREBBP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2022
R free: 0.2693
Average B factor: 44.856
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 277
Crystal growth procedure: 20% ethylene glycol
21% PEG6K
0.1M tris pH 8.3
0.125M lithium chloride
Matthews coefficient: 2.95
Solvent content (%): 58.37
Ligand: (4~{R})-6-[(~{E})-5-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)pent-1-enyl]-4-methyl-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one (OSN)
Ligand formula: C25 H31 N3 O2
Ligand molecular weight: 405.533
Ligand SMILES: CC1CC(=O)Nc2cccc(c2N1)C=CCCCN3CCCc4c3cc(cc4)OC
Ligand InChI: InChI=1S/C25H31N3O2/c1-18-16-24(29)27-22-11-6-9-20(25(22)26-18)8-4-3-5-14-28-15-7-10-19-12-13-21(30-2)17-23(19)28/h4,6,8-9,11-13,17-18,26H,3,5,7,10,14-16H2,1-2H3,(H,27,29)/b8-4+/t18-/m1/s1
Release date: 2020-04-15
Crystal Structure of Neutrophil Elastase Inhibited by Eap1 from S. aureus (PDB entry 8D4Q)
Macromolecule: Neutrophil elastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.37
Sequence length: 218 residues
Sequence: IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1809
R free: 0.2168
Average B factor: 48.5277
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M sodium citrate (pH 5.2),
12% (w/v) PEG-6000
Matthews coefficient: 3.23
Solvent content (%): 61.95
Release date: 2022-12-21
Crystal structure of human PCAF bromodomain in complex with fragment MB364 (fragment 5) (PDB entry 5FE4)
Macromolecule: Histone acetyltransferase KAT2B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMGKEKSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.18934
R free: 0.23175
Average B factor: 43.317
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8
Matthews coefficient: 3.36
Solvent content (%): 63.44
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: 2016-01-13
PXR in complex with P2X4 inhibitor compound 25 (PDB entry 6HTY)
Macromolecule: Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 344 residues
Sequence: MKKGHHHHHHGSERTGTQPLGVQGLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGITGSGGSGGSSHSSLTERHKILHRLLQEGSPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.1847
R free: 0.22611
Average B factor: 69.232
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 1 microliter protein at 12.1 mg/ml (in 20 millimolar Tris pH 7.8, 250 millimolar NaCl, 2.5 millimolar EDTA, 5% (v/v) glycerol, 5 mM DTT), preincubated with 10 millimolar compound 15 (from 200 millimolar stock in DMSO), mixed with 1 microliter of reservoir (100 mM imidazole pH 8.0, 17 % (v/v) MPD). Crystals additionally soaked in 20 millimolar compound 15 prior to data collection. cryo buffer 34% (v/v) MPD supplemented with 20 millimolar compound 15
Matthews coefficient: 2.54
Solvent content (%): 51.52
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: 2019-12-04
Structure of recombinant human butyrylcholinesterase in complex with a fluorescent coumarin-based probe (PDB entry 6R6V)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 526 residues
Sequence: IIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1921
R free: 0.2581
Average B factor: 62.179
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate
Matthews coefficient: 3.24
Solvent content (%): 61.99
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: 2020-01-15
Crystal structure of IRAK4 in complex with compound 11 (PDB entry 5UIR)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 323 residues
Sequence: MHHHHHHGGENLYFQGENKSLEVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.64
R work: 0.219
R free: 0.277
Average B factor: 61.84
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 1.6-1.8M Ammonium Citrate, pH 7.0
Matthews coefficient: 2.33
Solvent content (%): 47.29
Ligand: 5-(4-cyanophenyl)-3-[(propan-2-yl)oxy]naphthalene-2-carboxamide (8BY)
Ligand formula: C21 H18 N2 O2
Ligand molecular weight: 330.38
Ligand SMILES: CC(C)Oc1cc2c(cccc2c3ccc(cc3)C#N)cc1C(=O)N
Ligand InChI: InChI=1S/C21H18N2O2/c1-13(2)25-20-11-18-16(10-19(20)21(23)24)4-3-5-17(18)15-8-6-14(12-22)7-9-15/h3-11,13H,1-2H3,(H2,23,24)
Release date: 2017-05-24
Ternary complex crystal structure of DNA polymerase Beta with C:T mismatch at the primer terminus (PDB entry 5J2E)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2392
R free: 0.292
Average B factor: 26.4381
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
Matthews coefficient: 2.31
Solvent content (%): 46.75
Ligand: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE (DUP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
Release date: 2016-10-26
PARK7 with covalent inhibitor JYQ-88 (PDB entry 7PA3)
Macromolecule: Parkinson disease protein 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.2
Sequence length: 192 residues
Sequence: GPGMASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGGNLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGFGSKVTTHPLAKDKMMNGGHYTYSENRVEKDGLILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.42
R work: 0.1741
R free: 0.2138
Average B factor: 31.274
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Ammonium sulfate
0.1 M Bis-Tris pH 5.5
25% (w/v) PEG 3350
Matthews coefficient: 2.82
Solvent content (%): 56.44
Ligand: (3~{S})-~{N}-[5-[2-[(azanylidene-$l^{4}-azanylidene)amino]ethanoyl]-6,7-dihydro-4~{H}-[1,3]thiazolo[5,4-c]pyridin-2-yl]-1-(iminomethyl)pyrrolidine-3-carboxamide (6SI)
Ligand formula: C14 H23 N8 O2 S
Ligand molecular weight: 367.45
Ligand SMILES: C1CN(Cc2c1nc(s2)NC(=O)C3CCN(C3)C=N)C(=O)CN[NH2+]N
Ligand InChI: InChI=1S/C14H22N8O2S/c15-8-21-3-1-9(6-21)13(24)19-14-18-10-2-4-22(7-11(10)25-14)12(23)5-17-20-16/h8-9,15,17,20H,1-7,16H2,(H,18,19,24)/p+1/b15-8+/t9-/m0/s1
Release date: 2022-08-10
Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dATP soaked with MgCl2 for 1hr (PDB entry 4RQ7)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 343 residues
Sequence: MGMSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.20653
R free: 0.2609
Average B factor: 33.646
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Matthews coefficient: 2.36
Solvent content (%): 47.92
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2015-04-15
Carbonic Anhydrase II-mediated hydrolysis of selenolester (PDB entry 6XWZ)
Macromolecule: carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.38
R work: 0.1804
R free: 0.2042
Average B factor: 16.639
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: solution of 1.5-1.7 M sodium citrate, 0.1 M Tris pH 8.0
Matthews coefficient: 2.1
Solvent content (%): 41.34
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: 2021-02-03
Human Sirt6 in complex with ADP-ribose and fragment pyroglutamic acid (PDB entry 8AK5)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.1912
R free: 0.2217
Average B factor: 52.265
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Matthews coefficient: 2.32
Solvent content (%): 47
Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL
[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE (AR6)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
Release date: 2023-08-16
Human AURKC INCENP complex bound to BRD-7880 (PDB entry 6GR8)
Macromolecule: Aurora kinase C
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 274 residues
Sequence: GANSRRLTVDDFEIGRPLGKGKFGNVYLARLKESHFIVALKVLFKSQIEKEGLEHQLRREIEIQAHLQHPNILRLYNYFHDARRVYLILEYAPRGELYKELQKSDKLDEQRTATIIEELADALTYCHDKKVIHRDIKPENLLLGFRGEVKIADFGWSVHTPSLRRKTMCGTLDYLPPEMIEGRTYDEKVDLWCIGVLCYELLVGYPPFESASHSETYRRILKVDVRFPLSMPLGARDLISRLLRYQPLERLPLAQILKHPWVQAHSRRVLPPCA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.17648
R free: 0.21626
Average B factor: 18.932
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M sodium chloride, 25% PEG3350, 0.1 M HEPES pH 7.5
Matthews coefficient: 2.11
Solvent content (%): 41.73
Ligand: 1-[(2~{R},3~{S})-2-[[1,3-benzodioxol-5-ylmethyl(methyl)amino]methyl]-3-methyl-6-oxidanylidene-5-[(2~{S})-1-oxidanylpropan-2-yl]-3,4-dihydro-2~{H}-1,5-benzoxazocin-8-yl]-3-(4-methoxyphenyl)urea (F8Z)
Ligand formula: C32 H38 N4 O7
Ligand molecular weight: 590.667
Ligand SMILES: CC1CN(C(=O)c2cc(ccc2OC1CN(C)Cc3ccc4c(c3)OCO4)NC(=O)Nc5ccc(cc5)OC)C(C)CO
Ligand InChI: InChI=1S/C32H38N4O7/c1-20-15-36(21(2)18-37)31(38)26-14-24(34-32(39)33-23-6-9-25(40-4)10-7-23)8-12-27(26)43-30(20)17-35(3)16-22-5-11-28-29(13-22)42-19-41-28/h5-14,20-21,30,37H,15-19H2,1-4H3,(H2,33,34,39)/t20-,21-,30-/m0/s1
Release date: 2019-05-15