satarupa22/MacromolecularLigandDB huggingface dataset:
CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA EXTENDING AN 1,N6-ETHENODEOXYADENOSINE : dA PAIR BY INSERTING dTMPNPP OPPOSITE TEMPLATE dA (PDB entry 5DGB)
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): 1.79
R work: 0.1642
R free: 0.2122
Average B factor: 23
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES pH 5.5, 5mM magnesium chloride, 18% PEG 2000 MME
Matthews coefficient: 2.11
Solvent content (%): 41.58
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: 2016-06-08
DNA Polymerase Mu, dGTP:Ct Product State Ternary Complex, 10 mM Mg2+ (960min) (PDB entry 7KSY)
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): 1.577
R work: 0.1558
R free: 0.1695
Average B factor: 29.4751
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: 2.46
Solvent content (%): 49.99
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: 2021-12-01
Crystal structure of 1-hydroxy-4,6-dimethylpyridine-2(1H)-thione bound to human carbonic anhydrase II (PDB entry 4Q81)
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): 1.55
R work: 0.17409
R free: 0.19984
Average B factor: 12.477
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, temperature 291K
Matthews coefficient: 2.08
Solvent content (%): 40.84
Ligand: MERCURIBENZOIC ACID (MBO)
Ligand formula: C7 H5 Hg O2
Ligand molecular weight: 321.703
Ligand SMILES: c1cc(ccc1C(=O)O)[Hg]
Ligand InChI: InChI=1S/C7H5O2.Hg/c8-7(9)6-4-2-1-3-5-6;/h2-5H,(H,8,9);
Release date: 2015-03-11
DNA polymerase beta substrate complex with 8-oxoG:A at the primer terminus and incoming dCTP analog (PDB entry 5VEZ)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACGACGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.039
R work: 0.1873
R free: 0.2319
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM imidazole, 350 mM sodium chloride, 17% PEG3350
Matthews coefficient: 2.28
Solvent content (%): 46.09
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-05-10
Crystal structure of DUSP10 mutant_S95A (PDB entry 7Y4D)
Macromolecule: Dual specificity protein phosphatase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 149 residues
Sequence: SAELTPILPFLFLGNEQDAQDLDTMQRLNIGYVINVTTHLPLYHYEKGLFNYKRLPATDSNKQNLRQYFEEAFEFIEEAHQCGKGLLIHCQAGVARSATIVIAYLMKHTRMTMTDAYKFVKGKRPIISPNLNFMGQLLEFEEDLNNGVT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.18
R work: 0.1801
R free: 0.23
Average B factor: 49.4
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 283
Crystal growth procedure: 22.5% (w/v) PEG 3000, 100 mM Tris base /Hydrochloric acid, 
200 mM Calcium acetate
Matthews coefficient: 2.39
Solvent content (%): 48.56
Release date: 2023-06-21
Carbonic Anhydrase II in complex with Ferulic Acid (PDB entry 6MBY)
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): 1.496
R work: 0.1518
R free: 0.1742
Average B factor: 17.9939
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6 M NaCitrate, 50 mM Tris
Matthews coefficient: 2.1
Solvent content (%): 41.48
Ligand: 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID (FER)
Ligand formula: C10 H10 O4
Ligand molecular weight: 194.184
Ligand SMILES: COc1cc(ccc1O)C=CC(=O)O
Ligand InChI: InChI=1S/C10H10O4/c1-14-9-6-7(2-4-8(9)11)3-5-10(12)13/h2-6,11H,1H3,(H,12,13)/b5-3+
Release date: 2019-03-13
Nucleotide-binding domain 1 of the human cystic fibrosis transmembrane conductance regulator (CFTR) with dCTP (PDB entry 5TFJ)
Macromolecule: Cystic fibrosis transmembrane conductance regulator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.49
Sequence length: 229 residues
Sequence: SLTTTEVVMENVTAFWEEGGTPVLKDINFKIERGQLLAVAGSTGAGKTSLLMMIMGELEPSEGKIKHSGRISFCSQFSWIMPGTIKENIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNIVLGEGGITLSGGQRARISLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKMEHLKKADKILILHEGSSYFYGTFSELQNLQPDFSSKLMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.162
R free: 0.1853
Crystallization method: MICROBATCH
Crystallization pH: 7.5
Crystallization temperature (K): 279
Crystal growth procedure: Protein buffer: 150 mM NaCl, 10% (v/v) glycerol,10% (v/v) Ethylene glycol, 10mM MgCl2, 1 mM TCEP, and 20 mM Na-HEPES, pH 7.5. Precipitant buffer: 40% (v/v) PEG 400, 100 mM NH4Cl, and 100 mM MES, pH 6
Matthews coefficient: 2.38
Solvent content (%): 48.24
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: 2018-05-09
Aurora A Kinase in Complex with JNJ-7706621 in Space Group P6122 (PDB entry 5DT0)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 273 residues
Sequence: MGRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRATLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.2101
R free: 0.2248
Average B factor: 66.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 292
Crystal growth procedure: 100 mM HEPES pH 7.4, 200 mM magnesium sulfate, 2-20% PEG3350
Matthews coefficient: 2.64
Solvent content (%): 53.46
Ligand: 4-({5-amino-1-[(2,6-difluorophenyl)carbonyl]-1H-1,2,4-triazol-3-yl}amino)benzenesulfonamide (SKE)
Ligand formula: C15 H12 F2 N6 O3 S
Ligand molecular weight: 394.356
Ligand SMILES: c1cc(c(c(c1)F)C(=O)n2c(nc(n2)Nc3ccc(cc3)S(=O)(=O)N)N)F
Ligand InChI: InChI=1S/C15H12F2N6O3S/c16-10-2-1-3-11(17)12(10)13(24)23-14(18)21-15(22-23)20-8-4-6-9(7-5-8)27(19,25)26/h1-7H,(H2,19,25,26)(H3,18,20,21,22)
Release date: 2016-07-20
Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain. (PDB entry 5X8W)
Macromolecule: Nuclear receptor ROR-gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 258 residues
Sequence: EAPYASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPAGKLASLCSQHVERLQIFQHLHPIVVQAAFPPLYKELFSTETESPVGLSK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.21216
R free: 0.2296
Average B factor: 35.654
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Sodium acetate pH8.0, 4M ammonium acetate
Matthews coefficient: 2.35
Solvent content (%): 47.76
Release date: 2017-06-07
Human DNA polymerase eta-DNA ternary complex: reaction with 1 mM Mn2+ for 600s (PDB entry 5KFE)
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: 0.1729
R free: 0.2031
Average B factor: 21.847
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 17% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.1
Solvent content (%): 41.52
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: 2016-06-22
Crystal structure of Trk-A in complex with the Pan-Trk Kinase Inhibitor, compound 19. (PDB entry 6DKI)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 320 residues
Sequence: GSTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.1837
R free: 0.227
Average B factor: 39.71
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 294
Crystal growth procedure: Well volume: 20.0 uL

Well Ingredients:
Polymer: 9.0 %w/v (3.6 uL of stock 50.0 %w/v) PEG 3350
Buffer: 15.8 %v/v (3.16 uL of stock 100.0 %v/v) tacsimate (pH 8.00)
Additive: 0.025 M (5.0 uL of stock 0.1 M) TCEP hydrochloride

Plate setup temperature: 13 C
Plate incubation temperature: 21 C

Drop volume from well: 0.01 uL
Drop protein volume: 0.2 uL
Protein: 6.30 mg/mL
Matthews coefficient: 2.28
Solvent content (%): 46.08
Ligand: 6-amino-5-{[(3S)-4,4-difluoro-1-{[4-(trifluoromethoxy)phenyl]acetyl}pyrrolidin-3-yl]oxy}-N-methylpyridine-3-carboxamide (GOD)
Ligand formula: C20 H19 F5 N4 O4
Ligand molecular weight: 474.381
Ligand SMILES: CNC(=O)c1cc(c(nc1)N)OC2CN(CC2(F)F)C(=O)Cc3ccc(cc3)OC(F)(F)F
Ligand InChI: InChI=1S/C20H19F5N4O4/c1-27-18(31)12-7-14(17(26)28-8-12)32-15-9-29(10-19(15,21)22)16(30)6-11-2-4-13(5-3-11)33-20(23,24)25/h2-5,7-8,15H,6,9-10H2,1H3,(H2,26,28)(H,27,31)/t15-/m0/s1
Release date: 2018-07-11
HIPK2 kinase domain bound to CX-4945 (PDB entry 6P5S)
Macromolecule: Homeodomain-interacting protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 390 residues
Sequence: MGSSHHHHHHSSGENLYFQGSNSEGDYQLVQHEVLCSMTNTYEVLEFLGRGTFGQVVKCWKRGTNEIVAIKILKNHPSYARQGQIEVSILARLSTESADDYNFVRAYECFQHKNHTCLVFEMLEQNLYDFLKQNKFSPLPLKYIRPVLQQVATALMKLKSLGLIHADLKPENIMLVDPSRQPYRVKVIDFGSASHVSKAVCSTYLQSRYYRAPEIILGLPFCEAIDMWSLGCVIAELFLGWPLYPGASEYDQIRYISQTQGLPAEYLLSAGTKTTRFFNRDTDSPYPLWRLKTPDDHEAETGIKSKEARKYIFNCLDDMAQVNMTTDLEGSDMLVEKADRREFIDLLKKMLTIDADKRITPIETLNHPFVTMTHLLDFPHSTHVKSCFQN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.194
R work: 0.1977
R free: 0.238
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 3350, 0.2 M KSCN
Matthews coefficient: 2.84
Solvent content (%): 56.7
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: 2019-07-31
Ternary complex crystal structure of DNA polymerase Beta with (alpha, beta)-NH-(beta,gamma)-CH2-dTTP (PDB entry 4RT3)
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): 1.92
R work: 0.1798
R free: 0.2256
Average B factor: 35.2626
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, 18 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Matthews coefficient: 2.24
Solvent content (%): 45.18
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: 2015-07-01
Fragment-Based Discovery of a Novel Bruton's Tyrosine Kinase Inhibitor (PDB entry 7N5O)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 283 residues
Sequence: GPLPGKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.1786
R free: 0.1959
Average B factor: 16.232
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% polyethylene glycol 4000, 20% glycerol, 0.1M imidazole/MES, pH 6.5 and 0.12M alcohol mixture
Matthews coefficient: 2.21
Solvent content (%): 44.36
Ligand: IMIDAZOLE (IMD)
Ligand formula: C3 H5 N2
Ligand molecular weight: 69.085
Ligand SMILES: c1c[nH+]c[nH]1
Ligand InChI: InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)/p+1
Release date: 2021-09-08
Crystal structure of human PCNA in complex with APIM of human ZRANB3 (PDB entry 5YD8)
Macromolecule: Proliferating cell nuclear antigen
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 261 residues
Sequence: MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEGS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.21864
R free: 0.2645
Average B factor: 52.4
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350
Matthews coefficient: 2.18
Solvent content (%): 43.58
Release date: 2018-04-18
Crystal structure of human dihydroorotate dehydrogenase (DHODH) with 18L compound (PDB entry 5HIN)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 390 residues
Sequence: MGHHHHHHHHHHSSGHIDDDDKHMATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.16337
R free: 0.18217
Average B factor: 22.369
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M acetate, 40mM C11DAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8 M ammonium sulfate
Matthews coefficient: 3.42
Solvent content (%): 64.01
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2016-07-20
LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N53 i.e. 2-(5-([1,1'-biphenyl]-3-yl)-4-(1-(2-(piperidin-1-yl)ethoxy)ethyl)-1H-pyrazol-1-yl)isonicotinic acid (PDB entry 6DQD)
Macromolecule: Linked KDM5A Jmj Domain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.987
R work: 0.1887
R free: 0.2174
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.22
Solvent content (%): 44.52
Ligand: 2-[5-([1,1'-biphenyl]-3-yl)-4-{(1S)-1-[2-(piperidin-1-yl)ethoxy]ethyl}-1H-pyrazol-1-yl]pyridine-4-carboxylic acid (H67)
Ligand formula: C30 H32 N4 O3
Ligand molecular weight: 496.6
Ligand SMILES: CC(c1cnn(c1c2cccc(c2)c3ccccc3)c4cc(ccn4)C(=O)O)OCCN5CCCCC5
Ligand InChI: InChI=1S/C30H32N4O3/c1-22(37-18-17-33-15-6-3-7-16-33)27-21-32-34(28-20-26(30(35)36)13-14-31-28)29(27)25-12-8-11-24(19-25)23-9-4-2-5-10-23/h2,4-5,8-14,19-22H,3,6-7,15-18H2,1H3,(H,35,36)/t22-/m0/s1
Release date: 2019-06-12
Fragment-based discovery of pyrazolopyridones as JAK1 inhibitors with excellent subtype selectivity (PDB entry 6TPF)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 291 residues
Sequence: EVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.31
R work: 0.2633
R free: 0.3268
Average B factor: 65.906
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Matthews coefficient: 2.48
Solvent content (%): 50.51
Ligand: (1~{S})-2,2-bis(fluoranyl)-~{N}-[4-(3-methyl-6-oxidanylidene-2,7-dihydropyrazolo[3,4-b]pyridin-4-yl)cyclohexyl]cyclopropane-1-carboxamide (NTQ)
Ligand formula: C17 H20 F2 N4 O2
Ligand molecular weight: 350.363
Ligand SMILES: Cc1c2c(n[nH]1)NC(=O)C=C2C3CCC(CC3)NC(=O)C4CC4(F)F
Ligand InChI: InChI=1S/C17H20F2N4O2/c1-8-14-11(6-13(24)21-15(14)23-22-8)9-2-4-10(5-3-9)20-16(25)12-7-17(12,18)19/h6,9-10,12H,2-5,7H2,1H3,(H,20,25)(H2,21,22,23,24)/t9-,10-,12-/m0/s1
Release date: 2020-06-10
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1192341021 (PDB entry 7G89)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.901
R work: 0.2031
R free: 0.2436
Average B factor: 31.63
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.53
Solvent content (%): 51.35
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: 2023-07-12