satarupa22/MacromolecularLigandDB huggingface dataset:
The ubiquitin-associated domain of human thirty-eight negative kinase 1, fused to the 2TEL crystallization chaperone via a 2-glycine linker (PDB entry 9CPL)
Macromolecule: 2TEL/Non-receptor tyrosine-protein kinase TNK1 fusion protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 251 residues
Sequence: MGHHHHHHHHHHSIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLSPIDSNTFEMNGKALLLLTKEDFRYRSPHSGDELYELLQHILKQRPGGGGSTSIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLSPIDSNTFEMNGKALLLLTKEDFRYRSPHSGDVLYELLQHILGGELQRKIMEVELSVHGVTHQEAQTALGATGGDVVSAIRNLKVDQLFHLSSRSRADAWRILEHYQWDLSAASRYVLARP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2294
R free: 0.2634
Average B factor: 82.94
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 100mM BisTris, pH 6.0, 960mM Mg-formate
Matthews coefficient: 2.83
Solvent content (%): 56.48
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2024-08-14
Carbonic anhydrase IX-mimic in complex with 4-(3-quinolinyl)-benzenesulfonamide (PDB entry 5SZ7)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.776
R work: 0.161
R free: 0.1946
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 (%): 41.66
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
Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 0.5 mM Mn2+ for 1800s then with 10 mM Mn2+ for 90s (PDB entry 7U75)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1868
R free: 0.2215
Average B factor: 33.2246
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.11
Solvent content (%): 41.61
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2022-05-04
Crystal structure of USP7 in complex with UHRF1 (PDB entry 5C6D)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 322 residues
Sequence: SAHLYMQVQIVAEDQFCGHQGNDMYDEEKVKYTVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWPMQARSNGTKRPAMLDNEADGNKTMIELSDNENPWTIFLETVDPELAASGATLPKFDKDHDVMLFLKMYDPKTRSLNYCGHIYTPISCKIRDLLPVMCDRAGFIQDTSLILYEEVKPNLTERIQDYDVSLDKALDELMDGDIIVFQKDDPENDNSELPTAKEYFRDLYHRVDVIFCDKTIPNDPGFVVTLSNRMNYFQVAKTVAQRLNTDPMLLQFFKSQGYRDGPGNPLRHNYEGTLRDLLQFFKPRQPKKLYYQQL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.292
R work: 0.1858
R free: 0.2337
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM CHES (pH 9.0), 20% PEG8000
Matthews coefficient: 2.56
Solvent content (%): 51.92
Release date: 2015-09-09
PCSK9(deltaCRD) in complex with cyclic peptide 40 (PDB entry 6XIC)
Macromolecule: Proprotein convertase subtilisin/kexin type 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 121 residues
Sequence: EDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.377
R work: 0.2034
R free: 0.2214
Average B factor: 20.54
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG3350, 200mM CaCl2, 100mM MES pH 6
Matthews coefficient: 2.58
Solvent content (%): 52.36
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: 2020-11-18
Crystal structure of human carbonic anhydrase I in complex with the 3-(2,5-dimethylphenyl)-1-(2-hydroxy-5-sulfamoylphenyl)urea inhibitor (PDB entry 6FAF)
Macromolecule: Carbonic anhydrase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 261 residues
Sequence: MASPDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.2029
R free: 0.2571
Average B factor: 42.996
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 296
Crystal growth procedure: 28% PEG4000, 0.2 M Sodium acetate, Tris 100 mM
Matthews coefficient: 2.33
Solvent content (%): 47.15
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: 2018-10-10
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMSOA000341b (PDB entry 5QHU)
Macromolecule: Poly [ADP-ribose] polymerase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 183 residues
Sequence: SMFYGTVSSPDSGVYEMKIGSIIFQVASGDITKEEADVIVNSTSNSFNLKAGVSKAILECAGQNVERECSQQAQQRKNDYIITGGGFLRCKNIIHVIGGNDVKSSVSSVLQECEKKNYSSICLPAIGTGNAKQHPDKVAEAIIDAIEDFVQKGSAQSVKKVKVVIFLPQVLDVFYANMKKREG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.05
R work: 0.1416
R free: 0.1656
Average B factor: 14.12
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 80 mM KBr, 30 % PEG2kMME
Matthews coefficient: 1.99
Solvent content (%): 38.17
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2019-04-10
HDM2 in complex with compound 2 (PDB entry 7NA1)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 109 residues
Sequence: SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLYYLGQYIMTKRLYDEKQQHIVHCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSDSGTSVSEN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2554
R free: 0.3542
Average B factor: 45.284
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 285
Crystal growth procedure: 2 M ammonium sulfate, 100 mM citrate pH 3.5
Matthews coefficient: 2.48
Solvent content (%): 50.47
Ligand: 8-(1-benzothiophen-5-yl)-7-[(4-chlorophenyl)methyl]-6-{[(1R)-1-cyclopropylethyl]amino}-7H-purine-2-carboxylic acid (1GI)
Ligand formula: C26 H22 Cl N5 O2 S
Ligand molecular weight: 504.003
Ligand SMILES: CC(C1CC1)Nc2c3c(nc(n3Cc4ccc(cc4)Cl)c5ccc6c(c5)ccs6)nc(n2)C(=O)O
Ligand InChI: InChI=1S/C26H22ClN5O2S/c1-14(16-4-5-16)28-22-21-23(30-24(29-22)26(33)34)31-25(18-6-9-20-17(12-18)10-11-35-20)32(21)13-15-2-7-19(27)8-3-15/h2-3,6-12,14,16H,4-5,13H2,1H3,(H,33,34)(H,28,29,30)/t14-/m1/s1
Release date: 2021-11-10
X-RAY STRUCTURE OF CLK3-KD(GP-[275-632], NON-PHOS.)/CX-4945 AT 2.29A (PDB entry 6FYP)
Macromolecule: Dual specificity protein kinase CLK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 360 residues
Sequence: GPQSSKRSSRSVEDDKEGHLVCRIGDWLQERYEIVGNLGEGTFGKVVECLDHARGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVATRHYRPPEVILELGWAQPCDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSFHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29
R work: 0.2276
R free: 0.2666
Average B factor: 47.057
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG3350,0.2M Ammonium Sulfate, 0.1M TRIS
Matthews coefficient: 2.43
Solvent content (%): 49.47
Ligand: 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid (3NG)
Ligand formula: C19 H12 Cl N3 O2
Ligand molecular weight: 349.77
Ligand SMILES: c1cc(cc(c1)Cl)Nc2c3ccncc3c4ccc(cc4n2)C(=O)O
Ligand InChI: InChI=1S/C19H12ClN3O2/c20-12-2-1-3-13(9-12)22-18-15-6-7-21-10-16(15)14-5-4-11(19(24)25)8-17(14)23-18/h1-10H,(H,22,23)(H,24,25)
Release date: 2018-07-18
Human Brr2 Helicase Region in complex with C-tail deleted Jab1 and compound 18 (PDB entry 8BC8)
Macromolecule: U5 small nuclear ribonucleoprotein 200 kDa helicase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 1747 residues
Sequence: GAEFMDLDQGGEALAPRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPALKPKPFGSEEQLLPVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRRLDLVHTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQLLKPTLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKESIEEPSAKINVLLQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNRGWAQLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVVKKIEKKNFPFERLYDLNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKVELTITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLITFFVPVFEPLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLDLQPLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSKCISIEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYENIPIRHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQLSAELQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWSKDSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEERNALLQLTDSQIADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQLEREEEVTGPVIAPLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATGAHNYTLYFMSDAYMGCDQEYKFSVDVKEAETDSDSD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.39
R work: 0.2066
R free: 0.2447
Average B factor: 73.55
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1M Hepes-NaOH, 0.1M MgCl2, 8% PEG 3350
Matthews coefficient: 2.44
Solvent content (%): 49.53
Ligand: 3-azanyl-4-oxidanyl-benzenesulfonamide (QB6)
Ligand formula: C6 H8 N2 O3 S
Ligand molecular weight: 188.204
Ligand SMILES: c1cc(c(cc1S(=O)(=O)N)N)O
Ligand InChI: InChI=1S/C6H8N2O3S/c7-5-3-4(12(8,10)11)1-2-6(5)9/h1-3,9H,7H2,(H2,8,10,11)
Release date: 2023-03-08
Discovery of a Potent Cyclophilin Inhibitor (Compound 5) based on Structural Simplification of Sanglifehrin A (PDB entry 5T9W)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1508
R free: 0.1841
Average B factor: 14.54
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.05 M monobasic potassium phosphate
20% (w/v) PEG 8000
Matthews coefficient: 2.62
Solvent content (%): 53.1
Ligand: 3-[(3-hydroxyphenyl)methyl]-6-(propan-2-yl)-19-oxa-1,4,7,25-tetraazabicyclo[19.3.1]pentacosa-13,15-diene-2,5,8,20-tetrone (78E)
Ligand formula: C30 H42 N4 O6
Ligand molecular weight: 554.678
Ligand SMILES: CC(C)C1C(=O)NC(C(=O)N2CCCC(N2)C(=O)OCCC=CC=CCCCCC(=O)N1)Cc3cccc(c3)O
Ligand InChI: InChI=1S/C30H42N4O6/c1-21(2)27-28(37)31-25(20-22-13-11-14-23(35)19-22)29(38)34-17-12-15-24(33-34)30(39)40-18-10-8-6-4-3-5-7-9-16-26(36)32-27/h3-4,6,8,11,13-14,19,21,24-25,27,33,35H,5,7,9-10,12,15-18,20H2,1-2H3,(H,31,37)(H,32,36)/b4-3+,8-6+/t24-,25-,27-/m0/s1
Release date: 2017-01-25
MTH1 substrate recognition: Complex with a methylbenzimidazolyl acetamide. (PDB entry 5FSM)
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: MGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.1795
R free: 0.2101
Average B factor: 17.31
Crystal growth procedure: 25% (W/V) PEG3350 200MM LITHIUM SULPHATE 100MM SODIUM ACETATE PH4.5
Matthews coefficient: 2.01
Solvent content (%): 38.74
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2016-07-20
Aurora A kinase in complex with TPX2-inhibitor 7 (PDB entry 8C1G)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 265 residues
Sequence: MGRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.199
R free: 0.225
Average B factor: 45.22
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG5000 MME, 0.1M (NH4)2SO4, 0.1 M MES 6.5: soaking: 31.5% PEG5000 MME, 0.09M (NH4)2SO4, 0.09 M MES 6.5, 10% DMSO, 5 mM compound
Matthews coefficient: 2.52
Solvent content (%): 51.28
Ligand: 4-(4-chlorophenyl)-~{N}-(dimethylsulfamoyl)-7-methyl-1~{H}-indole-6-carboxamide (T3I)
Ligand formula: C18 H18 Cl N3 O3 S
Ligand molecular weight: 391.872
Ligand SMILES: Cc1c(cc(c2c1[nH]cc2)c3ccc(cc3)Cl)C(=O)NS(=O)(=O)N(C)C
Ligand InChI: InChI=1S/C18H18ClN3O3S/c1-11-15(18(23)21-26(24,25)22(2)3)10-16(14-8-9-20-17(11)14)12-4-6-13(19)7-5-12/h4-10,20H,1-3H3,(H,21,23)
Release date: 2024-01-10
Human catalytic MMP-12 in complex with 5-(1,2-dithiolan-3-yl)-N-(3-hydroxypropyl)pentanamide (PDB entry 5N5K)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 156 residues
Sequence: VWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.16721
R free: 0.22736
Average B factor: 16.315
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris-HCl, 20% PEG 6000
Matthews coefficient: 2.15
Solvent content (%): 42.88
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: 2017-11-01
Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant at pH 4.0 (PDB entry 7A2T)
Macromolecule: Tyrosine-protein kinase Fyn
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 61 residues
Sequence: GVTLFVALYDYEARTEDDLSFHKGEKFQIVNNTEGDWWLAHSLTTGETGYIPSNYVAPVDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.22
R work: 0.1702
R free: 0.2026
Average B factor: 17.2614
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 298
Crystal growth procedure: 1 ammonium sulfate, 0.1M sodium acetate
Matthews coefficient: 2.01
Solvent content (%): 38.87
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2021-08-25
Crystal structure of ATP-dependent RNA helicase DDX42 (PDB entry 8DPE)
Macromolecule: ATP-dependent RNA helicase DDX42
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 444 residues
Sequence: MGHHHHHHPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMHQIRKSEYTQPTPIQCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDGPIAVIVCPTRELCQQIHAECKRFGKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGRLIDHVKKKATNLQRVSYLVFDEADRMFDMGFEYQVRSIASHVRPDRQTLLFSATFRKKIEKLARDILIDPIRVVQGDIGEANEDVTQIVEILHSGPSKWNWLTRRLVEFTSSGSVLLFVTKKANAEELANNLKQEGHNLGLLHGDMDQSERNKVISDFKKKDIPVLVATDVAARGLDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDLVRNLEGANQHVSKELLDLAMQNAWFRKSRFKGG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.531
R work: 0.2121
R free: 0.2552
Average B factor: 25.6866
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1 uL 8 mg/mL DDX42 (in 25 mM Tris, pH 7.5, 300 mM sodium chloride, 1 mM TCEP) + 1 uL reservoir solution (6-10% PEG8000, 0.1 M Tris, pH 8.5-9.0)
Matthews coefficient: 2.11
Solvent content (%): 41.78
Release date: 2022-08-24
Human Adenosine deaminase-like protein in complex with compound AT8001 (PDB entry 8QCH)
Macromolecule: Adenosine deaminase-like protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4
Sequence length: 355 residues
Sequence: MIEAEEQQPCKTDFYSELPKVELHAHLNGSISSHTMKKLIAQKPDLKIHDQMTVIDKGKKRTLEECFQMFQTIHQLTSSPEDILMVTKDVIKEFADDGVKYLELRSTPRRENATGMTKKTYVESILEGIKQSKQENLDIDVRYLIAVDRRGGPLVAKETVKLAEEFFLSTEGTVLGLDLSGDPTVGQAKDFLEPLLEAKKAGLKLALHLSEIPNQKKETQILLDLLPDRIGHGTFLNSGEGGSLDLVDFVRQHRIPLELCLTSNVKSQTVPSYDQHHFGFWYSIAHPSVICTDDKGVFATHLSQEYQLAAETFNLTQSQVWDLSYESINYIFASDSTRSELRKKWNHLKPRVLHI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.442
R work: 0.2143
R free: 0.2431
Average B factor: 50.42
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 2000 mM Ammonium sulfate
100 mM Sodium cacodylate/HCl
200 mM Sodium chloride
Matthews coefficient: 2.35
Solvent content (%): 47.58
Ligand: [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate (EIF)
Ligand formula: C11 H15 F N5 O7 P
Ligand molecular weight: 379.238
Ligand SMILES: CC1(C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)O)O)F
Ligand InChI: InChI=1S/C11H15FN5O7P/c1-11(12)6(18)4(2-23-25(20,21)22)24-9(11)17-3-14-5-7(17)15-10(13)16-8(5)19/h3-4,6,9,18H,2H2,1H3,(H2,20,21,22)(H3,13,15,16,19)/t4-,6-,9-,11-/m1/s1
Release date: 2024-07-31
Co-crystal structure of SPR with compound 5 (PDB entry 6USN)
Macromolecule: Sepiapterin reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.153
Sequence length: 263 residues
Sequence: GSMEGGLGRAVCLLTGASRGFGRTLAPLLASLLSPGSVLVLSARNDEALRQLEAELGAERSGLRVVRVPADLGAEAGLQQLLGALRELPRPKGLQRLLLINNAGSLGDVSKGFVDLSDSTQVNNYWALNLTSMLCLTSSVLKAFPDSPGLNRTVVNISSLCALQPFKGWALYCAGKAARDMLFQVLALEEPNVRVLNYAPGPLDTDMQQLARETSVDPDMRKGLQELKAKGKLVDCKVSAQKLLSLLEKDEFKSGAHVDFYDK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.773
R work: 0.1681
R free: 0.2011
Average B factor: 53.1271
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M MES pH 6.5,
2.3 M Ammonium Sulfate,
2% PEG1000
Matthews coefficient: 4.91
Solvent content (%): 74.96
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2019-12-11
Crystal structure of QE-hNTAQ1 C28S (PDB entry 8JJF)
Macromolecule: Protein N-terminal glutamine amidohydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.122
Sequence length: 204 residues
Sequence: QEMEGNGPAAVHYQPASPPRDACVYSSCYSEENVWKLCEYIKNHDQYPLEECYAVFISNERKMIPIWKQQARPGDGPVIWDYHVVLLHVSSGGQSFIYDLDTVLPFPCLFDTYVEDAIKSDDDIHPQFRRKFRVICADSYLKNFASDRSHMKDSSGNWREPPPPYPCIETGDSKMNLNDFISMDPKVGWGAVYTLSEFTHRFGS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51
R work: 0.1728
R free: 0.1899
Average B factor: 18.9
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295.15
Crystal growth procedure: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, and 25 % (w/v) Polyethylene glycol (PEG) 3350
Matthews coefficient: 2.49
Solvent content (%): 50.57
Release date: 2024-06-26