satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of nucleotide-binding domain 2 (NBD2) of the human Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) (PDB entry 6UK1)
Macromolecule: Cystic fibrosis transmembrane conductance regulator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.6.1.6
Sequence length: 229 residues
Sequence: DIWPSGGQMTVKDLTAKYTEGGNAILENISFSISPGQRVGLLGRTGSGKSTLLLAFLRLLNTEGEIQIDGVSWDSITLEQWRKAFGVIPQDVFIFSGTFRKNLDPNEQWSDQEIWKVADEVGLRSVIEQFPGGLDFVLVDGGCVLSHGHKQLMCLARAVLSKAKILLLDEPSAHLDPVTYQIIRRTLKQAFADCTVILCEARIEAMLECDQFLVIEENKVRQYDSIQKL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.693
R work: 0.2734
R free: 0.3036
Average B factor: 52.7125
Crystallization method: MICROBATCH
Crystallization temperature (K): 277
Crystal growth procedure: 24% PEG 8000, 100 mM Li2SO4, 10mM NaBr, 100 mM Bis-Tris Propane pH 6.0
Matthews coefficient: 2.9
Solvent content (%): 57.58
Ligand: ADENOSINE-5'-TRIPHOSPHATE (ATP)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2020-10-07
Crystal structure of the catalytic domain of MMP-9 in complex with a selective sugar-conjugated arylsulfonamide carboxylate water-soluble inhibitor (DC27). (PDB entry 5I12)
Macromolecule: Matrix metalloproteinase-9,Matrix metalloproteinase-9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.35
Sequence length: 157 residues
Sequence: DLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGVGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.188
R free: 0.228
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.25
Crystallization temperature (K): 293
Crystal growth procedure: protein solution: 415.2 micro-M MMP9 WT + 0.120 M Acetohydroxamic acid in 20 mM Tris pH 7.0 with 0.001 M inhibitor DC27 and 10% DMSO.
precipitant: 40% MPEG 5K ; 0.1 M bicine ; pH 7.25
sitting drops of 1 micro-L protein solution and 1 micro-L precipitant solution.
cryoprotectant:_40% cryomix CM2 (25 % di-ethylene glycol + 25 % glycerol + 25 % 1,2-propanediol), 10% PEG 10K, 200 milli-M NaCl, 100 milli-M Na propionate, Na cacodylate, Bis-Tris-propane (PCTP 50% acid/50% basic) pH 7.0 + 0.001 M inhibitor DC27.
Matthews coefficient: 2.1
Solvent content (%): 41.5
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: 2016-07-06
Crystal structure of highly glycosylated human leukocyte elastase in complex with a thiazolidinedione inhibitor (PDB entry 6F5M)
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: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1758
R free: 0.2336
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: HLE from human blood was purchased from SERVA as a lyophilisate in the presence of sodium acetate puffer, pH 5.5. The lyophilisate was disolved in water so that the HLE concentration was 5 mg/ml (170 micromolar) and the acetate concentration 250 millimolar. 120 microliter dissolved HNE lysophilisate was mixed with 6 microliter inhibitor solution (10 mM in DMSO). 1 microliter of the resulting HLE/inhibitor mixture was mixed with 0.5 microliter reservoir solution which was composed of 20 % PEG MME 5000, 0.2 M potassium sulphate. Repeated seeding was necessary to get usable crystals. In the final seeding step the reservoir was composed of 20 % PEG MME 5000, 0.2 M sodium sulphate.
Matthews coefficient: 2.68
Solvent content (%): 54.16
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: 2018-08-08
GTPase HRAS under 650 MPa pressure (PDB entry 7OGC)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 166 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.161
R free: 0.221
Average B factor: 18.39
Crystallization method: BATCH MODE
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 40 mM Tris HCL, 10 mM MgCl2, 2 mM DTE, 26-30 % PEG-400
Matthews coefficient: 1.91
Solvent content (%): 35.6
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2022-02-09
Crystal Structure of Mek1NES peptide bound to CRM1(E571K) (PDB entry 6X2X)
Macromolecule: GTP-binding nuclear protein Ran
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 216 residues
Sequence: MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.458
R work: 0.2
R free: 0.25
Average B factor: 41.8216
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 273
Crystal growth procedure: 17% (weight/vol) PEG3350, 100 mM Bis-Tris (pH 6.4), 200 mM ammonium nitrate, and 10 mM Spermine HCl
Matthews coefficient: 2.7
Solvent content (%): 54.48
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2020-07-01
Kinase domain of ALK2-K492A/K493A with LDN-193189 (PDB entry 6UNS)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 330 residues
Sequence: MSYYHHHHHHHHHHDYDIPTTENLYFQGAMGQRTVARQITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIAATLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2123
R free: 0.2618
Average B factor: 37.84
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: 0.05 M PIPES pH 7, 0.01 M DTT, 10 %w/v PEG 4000
Matthews coefficient: 2.27
Solvent content (%): 45.91
Ligand: 4-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline (LDN)
Ligand formula: C25 H22 N6
Ligand molecular weight: 406.482
Ligand SMILES: c1ccc2c(c1)c(ccn2)c3cnn4c3ncc(c4)c5ccc(cc5)N6CCNCC6
Ligand InChI: InChI=1S/C25H22N6/c1-2-4-24-22(3-1)21(9-10-27-24)23-16-29-31-17-19(15-28-25(23)31)18-5-7-20(8-6-18)30-13-11-26-12-14-30/h1-10,15-17,26H,11-14H2
Release date: 2021-07-07
TGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D) IN COMPLEX WITH N-{4-[3-(6-METHOXYPYRIDIN-3-YL)-1H-PYRROLO[3,2-B]PYRIDIN-2-YL]PYRIDIN-2-YL}ACETAMIDE (PDB entry 5QIL)
Macromolecule: TGF-beta receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 307 residues
Sequence: GHMTIARDIVLQESIGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIYQTVMLRHENILGFIAADNKDNGTWTQLWLVSDYHEHGSLFDYLNRYTVTVEGMIKLALSTASGLAHLHMEIVGTQGKPAIAHRDLKSKNILVKKNGTCCIADLGLAVRHDSATDTIDIAPNHRVGTKRYMAPEVLDDSINMKHFESFKRADIYAMGLVFWEIARRCSIGGIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQEGIKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1692
R free: 0.2098
Average B factor: 27.44
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 277
Crystal growth procedure: 23%(w/v) PEG3350, 3%(v/v) glcyerol
Matthews coefficient: 2.03
Solvent content (%): 39.35
Ligand: N-{4-[3-(6-methoxypyridin-3-yl)-1H-pyrrolo[3,2-b]pyridin-2-yl]pyridin-2-yl}acetamide (J2V)
Ligand formula: C20 H17 N5 O2
Ligand molecular weight: 359.381
Ligand SMILES: CC(=O)Nc1cc(ccn1)c2c(c3c([nH]2)cccn3)c4ccc(nc4)OC
Ligand InChI: InChI=1S/C20H17N5O2/c1-12(26)24-16-10-13(7-9-21-16)19-18(14-5-6-17(27-2)23-11-14)20-15(25-19)4-3-8-22-20/h3-11,25H,1-2H3,(H,21,24,26)
Release date: 2018-10-31
Human CLOCK PAS-A domain (PDB entry 6QPJ)
Macromolecule: Circadian locomoter output cycles protein kaput
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 161 residues
Sequence: MSNEEFTQLMLEALDGFFLAIMTDGSIIYVSESVTSLLEHLPSDLVDQSIFNFIPEGEHSEVYKILSTHLLESDSLTPEYLKSKNQLEFCCHMLRGTIDPKEPSTYEYVKFIGNFKSLNSVSSSAHNGFEGTIQRTHRPSYEDRVCFVATVRLATPQFIKE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.315
R work: 0.1796
R free: 0.2425
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 20 mM MES pH 6.5
0.1M Magnesium sulfate
20 % PEG 3350
Matthews coefficient: 2.15
Solvent content (%): 42.82
Release date: 2019-09-25
Crystal structure of CREBBP bromodomain complexed with KD341 (PDB entry 6SQE)
Macromolecule: CREB-binding protein
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): 1.506
R work: 0.1607
R free: 0.1906
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.2M MgCl2, 25% PEG 3350, 0.1M BisTris pH 5.5
Matthews coefficient: 2.29
Solvent content (%): 46.28
Ligand: ~{N}-[3-[(5-ethanoyl-2-ethoxy-phenyl)carbamoyl]-5-(1-methylpyrazol-3-yl)phenyl]-5-[(4-methylpiperazin-1-yl)methyl]furan-2-carboxamide (LSZ)
Ligand formula: C32 H36 N6 O5
Ligand molecular weight: 584.665
Ligand SMILES: CCOc1ccc(cc1NC(=O)c2cc(cc(c2)NC(=O)c3ccc(o3)CN4CCN(CC4)C)c5ccn(n5)C)C(=O)C
Ligand InChI: InChI=1S/C32H36N6O5/c1-5-42-29-8-6-22(21(2)39)19-28(29)34-31(40)24-16-23(27-10-11-37(4)35-27)17-25(18-24)33-32(41)30-9-7-26(43-30)20-38-14-12-36(3)13-15-38/h6-11,16-19H,5,12-15,20H2,1-4H3,(H,33,41)(H,34,40)
Release date: 2020-09-30
Human cathepsin B in complex with the carbamate inhibitor 31 (PDB entry 8B5F)
Macromolecule: Cathepsin B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.1
Sequence length: 255 residues
Sequence: KLPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDLLTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGARPPCTGEGDTPKCSKICEPGYSPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGIPRTD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1747
R free: 0.2051
Average B factor: 23.241
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Sodium Acetate pH 5.5, 30% PEG 5000 MME
Matthews coefficient: 2.09
Solvent content (%): 41.25
Ligand: (2S)-2-[[(2S)-2-[[3-chloranyl-4-[[3-phenyl-2-(phenylmethyl)propanoyl]amino]phenoxy]carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid (P9U)
Ligand formula: C41 H44 Cl N3 O6
Ligand molecular weight: 710.258
Ligand SMILES: c1ccc(cc1)CC(Cc2ccccc2)C(=O)Nc3ccc(cc3Cl)OC(=O)NC(CC4CCCCC4)C(=O)NC(Cc5ccccc5)C(=O)O
Ligand InChI: InChI=1S/C41H44ClN3O6/c42-34-27-33(21-22-35(34)43-38(46)32(23-28-13-5-1-6-14-28)24-29-15-7-2-8-16-29)51-41(50)45-36(25-30-17-9-3-10-18-30)39(47)44-37(40(48)49)26-31-19-11-4-12-20-31/h1-2,4-8,11-16,19-22,27,30,32,36-37H,3,9-10,17-18,23-26H2,(H,43,46)(H,44,47)(H,45,50)(H,48,49)/t36-,37-/m0/s1
Release date: 2023-10-04
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1198180782 (PDB entry 7G8H)
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): 1.67
R work: 0.193
R free: 0.2177
Average B factor: 33.19
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 (%): 51.3
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
Crystal structure of Rev7-K44A/R124A/A135D in complex with Rev3-RBM2 (residues 1988-2014) (PDB entry 6BCD)
Macromolecule: Mitotic spindle assembly checkpoint protein MAD2B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 227 residues
Sequence: MGSSHHHHHHSQDPNSMTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQARKKYNVPVQMSCHPELNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLAAFILKISVCDDVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKGS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1749
R free: 0.1974
Average B factor: 29.8026
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.25
Crystallization temperature (K): 289.15
Crystal growth procedure: well solution containing 100 mM sodium citrate, 1.6 M ammonium sulfate, pH=5.25 was mixed at 1:1 ratio with protein at 45 mg/mL in 5 mM HEPES, 100 mM NaCl, 10 mM DTT, pH=7.4
Matthews coefficient: 2.7
Solvent content (%): 53.2
Release date: 2018-08-01
Crystal structure of human RECQL5 helicase in complex with ADP/Mg. (PDB entry 5LB3)
Macromolecule: ATP-dependent DNA helicase Q5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 445 residues
Sequence: MSDPERRVRSTLKKVFGFDSFKTPLQESATMAVVKGNKDVFVCMPTGAGKSLCYQLPALLAKGITIVVSPLIALIQDQVDHLLTLKVRVSSLNSKLSAQERKELLADLEREKPQTKILYITPEMAASSSFQPTLNSLVSRHLLSYLVVDEAHCVSQWGHDFRPDYLRLGALRSRLGHAPCVALTATATPQVQEDVFAALHLKKPVAIFKTPCFRANLFYDVQFKELISDPYGNLKDFCLKALGQEADKGLSGCGIVYCRTREACEQLAIELSCRGVNAKAYHAGLKASERTLVQNDWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGRAGRDGKPSWCRLYYSRNDRDQVSFLIRKEVAKLQEKRGNKASDKATIMAFDALVTFCEELGCRHAAIAKYFGDALPACAKGCDHCQNPTAVRRRLEALERSSSW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1949
R free: 0.2335
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 23% PEG6K, 0.15M lithium chloride, 2.5% ethylene glycol
Matthews coefficient: 2.41
Solvent content (%): 48.94
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: 2016-07-06
Complex structure of JMJD5 and Symmetric Dimethyl-Arginine (SDMA) (PDB entry 6AX3)
Macromolecule: Lysine-specific demethylase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.27
Sequence length: 236 residues
Sequence: GSGVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.206
R free: 0.2591
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.0
8% PEG 3350
Matthews coefficient: 2.26
Solvent content (%): 45.65
Ligand: N3, N4-DIMETHYLARGININE (2MR)
Ligand formula: C8 H18 N4 O2
Ligand molecular weight: 202.254
Ligand SMILES: CNC(=NC)NCCCC(C(=O)O)N
Ligand InChI: InChI=1S/C8H18N4O2/c1-10-8(11-2)12-5-3-4-6(9)7(13)14/h6H,3-5,9H2,1-2H3,(H,13,14)(H2,10,11,12)/t6-/m0/s1
Release date: 2018-02-28
Thrombin in Complex with a D-Phe-Pro-diaminopyridine derivative (PDB entry 6HSX)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1623
R free: 0.1835
Average B factor: 28.05
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM Sodium dihydrogen phosphate pH 7.5, 350 mM NaCl, 27% PEG 8000
Matthews coefficient: 2.54
Solvent content (%): 51.6
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: 2019-10-23
Human Carbonic Anhydrase II in complex with N-(2-aminophenyl)-4-((2-oxo-2-((4-sulfamoylphenethyl)amino)ethyl)amino)benzamide (PDB entry 7QRK)
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): 1.428
R work: 0.1515
R free: 0.1696
Average B factor: 15.347
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Matthews coefficient: 2.08
Solvent content (%): 40.79
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: 2023-01-25
Carbonic anhydrase II in complex with Hit3-t1 (MH172) (PDB entry 7OYP)
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): 1.05
R work: 0.1175
R free: 0.1343
Average B factor: 13.688
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: 2.09
Solvent content (%): 41.25
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: 2023-01-18
Structure-based drug design of novel ASK1 inhibitors using a fully integrated lead optimization strategy (PDB entry 5V24)
Macromolecule: Mitogen-activated protein kinase kinase kinase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 271 residues
Sequence: LLEYDYEYDENGDRVVLGKGTYGIVYAGRDLSNQVRIAIKEIPERDSRYSQPLHEEIALHKHLKHKNIVQYLGSFSENGFIKIFMEQVPGGSLSALLRSKWGPLKDNEQTIGFYTKQILEGLKYLHDNQIVHRDIKGDNVLINTYSGVLKISDFGTSKRLAGINPCTETFTGTLQYMAPEIIDKGPRGYGKAADIWSLGCTIIEMATGKPPFYELGEPQAAMFKVGMFKVHPEIPESMSAEAKAFILKCFEPDPDKRACANDLLVDEFLKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2343
R free: 0.2659
Average B factor: 69.477
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 6% polyethylene glycol 2000 MME, 0.1M MES, pH 6.0
Matthews coefficient: 3.14
Solvent content (%): 60.84
Ligand: 2-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]-N-(pyridin-2-yl)-1,3-thiazole-4-carboxamide (8V7)
Ligand formula: C14 H14 N6 O S
Ligand molecular weight: 314.366
Ligand SMILES: CC(C)n1cnnc1c2nc(cs2)C(=O)Nc3ccccn3
Ligand InChI: InChI=1S/C14H14N6OS/c1-9(2)20-8-16-19-12(20)14-17-10(7-22-14)13(21)18-11-5-3-4-6-15-11/h3-9H,1-2H3,(H,15,18,21)
Release date: 2017-03-29
Crystal structure of human Cdk13/Cyclin K in complex with the inhibitor THZ531 (PDB entry 7NXJ)
Macromolecule: Cyclin-K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 268 residues
Sequence: GMKENKENSSPSVTSANLDHTKPCWYWDKKDLAHTPSQLEGLDPATEARYRREGARFIFDVGTRLGLHYDTLATGIIYFHRFYMFHSFKQFPRYVTGACCLFLAGKVEETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQTIKFDLQVEHPYQFLLKYAKQLKGDKNKIQKLVQMAWTFVNDSLCTTLSLQWEPEIIAVAVMYLAGRLCKFEIQEWTSKPMYRRWWEQFVQDVPVDVLEDICHQILDLYSQGKQQMPH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.2121
R free: 0.2518
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES (pH 6.8), 24% PEG 3350, 0.2 M MgCl2
Matthews coefficient: 2.36
Solvent content (%): 47.83
Ligand: N-[4-[(3R)-3-[[5-chloranyl-4-(1H-indol-3-yl)pyrimidin-2-yl]amino]piperidin-1-yl]carbonylphenyl]-4-(dimethylamino)butanamide (5I1)
Ligand formula: C30 H34 Cl N7 O2
Ligand molecular weight: 560.09
Ligand SMILES: CN(C)CCCC(=O)Nc1ccc(cc1)C(=O)N2CCCC(C2)Nc3ncc(c(n3)c4c[nH]c5c4cccc5)Cl
Ligand InChI: InChI=1S/C30H34ClN7O2/c1-37(2)15-6-10-27(39)34-21-13-11-20(12-14-21)29(40)38-16-5-7-22(19-38)35-30-33-18-25(31)28(36-30)24-17-32-26-9-4-3-8-23(24)26/h3-4,8-9,11-14,17-18,22,32H,5-7,10,15-16,19H2,1-2H3,(H,34,39)(H,33,35,36)/t22-/m1/s1
Release date: 2021-05-12