satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human carbonic anhydrase II in complex with (R)-4-(6,7-dihydroxy-1-phenyl-3,4-tetrahydroisoquinoline-1H-2-carbonyl)benzenesulfonamide. (PDB entry 5N0D)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 262 residues
Sequence: MGMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.173
R free: 0.209
Average B factor: 12.9
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 0.1 M Tris-HCl, pH 8.5.
Matthews coefficient: 2.06
Solvent content (%): 40.4
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: 2017-05-10
p38(alpha) MAP kinase with the activation loop of ERK2 (PDB entry 6QYX)
Macromolecule: Mitogen-activated protein kinase 14,Mitogen-activated protein kinase 1,Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 366 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.18485
R free: 0.24233
Average B factor: 37.548
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES pH 7.5, 
0.2 M KF, 
13%-17% (w/v) PEG 3350, 
25 mM beta-D-octyl glucoside (bOG)
Matthews coefficient: 2.3
Solvent content (%): 46.51
Ligand: octyl beta-D-glucopyranoside (BOG)
Ligand formula: C14 H28 O6
Ligand molecular weight: 292.369
Ligand SMILES: CCCCCCCCOC1C(C(C(C(O1)CO)O)O)O
Ligand InChI: InChI=1S/C14H28O6/c1-2-3-4-5-6-7-8-19-14-13(18)12(17)11(16)10(9-15)20-14/h10-18H,2-9H2,1H3/t10-,11-,12+,13-,14-/m1/s1
Release date: 2020-04-01
V308E mutant of cytochrome P450 2D6 complexed with thioridazine (PDB entry 6CSB)
Macromolecule: Cytochrome P450 2D6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.1
Sequence length: 479 residues
Sequence: MAKKTSSKGKLPPGPLPLPGLGNLLHVDFQNTPYCFDQLRRRFGDVFSLQLAWTPVVVLNGLAAVREALVTHGEDTADRPPVPITQILGFGPRSQGVFLARYGPAWREQRRFSVSTLRNLGLGKKSLEQWVTEEAACLCAAFANHSGRPFRPNGLLDKAVSNVIASLTCGRRFEYDDPRFLRLLDLAQEGLKEESGFLREVLNAVPVLLHIPALAGKVLRFQKAFLTQLDELLTEHRMTWDPAQPPRDLTEAFLAEMEKAKGNPESSFNDENLRIVVADLFSAGMETTSTTLAWGLLLMILHPDVQRRVQQEIDDVIGQVRRPEMGDQAHMPYTTAVIHEVQRFGDIVPLGVTHMTSRDIEVQGFRIPKGTTLITNLSSVLKDEAVWEKPFRFHPEHFLDAQGHFVKPEAFLPFSAGRRACLGEPLARMELFLFFTSLLQHFSFSVPTGQPRPSHHGVFAFLVSPSPYELCAVPRHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.394
R work: 0.193
R free: 0.2292
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: mixing 1.5 ul of the protein solution, 0.25 ul 70 mM HEGA-10, and 0.3 ul of the reservoir solution containing 10-20% of PEG 400, 0.1 M cacodylate, pH 7.0, 2 mM ZnSO4, and 200 mM MgAc2
Matthews coefficient: 3.23
Solvent content (%): 61.89
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2019-03-27
Human PRPF4B bound to benzothiophene inhibitor 329 (PDB entry 6PK6)
Macromolecule: Serine/threonine-protein kinase PRP4 homolog
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 351 residues
Sequence: SMDFKENPNLRDNWTDAEGYYRVNIGEVLDKRYNVYGYTGQGVFSNVVRARDNARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCLRLFRHFYHKQHLCLVFEPLSMNLREVLKKYGKDVGLHIKAVRSYSQQLFLALKLLKRCNILHADIKPDNILVNESKTILKLCDFGSASHVADNDITPYLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNHMLKLAMDLKGKMPNKMIRKGVFKDQHFDQNLNFMYIEVDKVTEREKVTVMSTINPTKDLLADLIGCQRLPEDQRKKVHQLKDLLDQILMLDPAKRISINQALQHAFIQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.189
R free: 0.2165
Average B factor: 42.55
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M CAPSO pH 9.5, 20% PEG 8,000
Matthews coefficient: 3.21
Solvent content (%): 61.63
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: 2019-08-28
Coagulation factor XI protease domain in complex with active site inhibitor (PDB entry 6TS6)
Macromolecule: Coagulation factor XI
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 238 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.33
R work: 0.1929
R free: 0.2102
Average B factor: 16.81
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH5.5, 25% w/v Polyethylene glycol 3350
Matthews coefficient: 2.26
Solvent content (%): 45.6
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: 2020-07-08
Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand A1120 and engineered binding scaffold (PDB entry 6QBA)
Macromolecule: Retinol-binding protein 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 185 residues
Sequence: GPERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEGLFLQDNIVAEFSVDETGQMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKGNDDHWIVDTDYDTYAVQYSCRLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQEELCLARQYRLIVHNGYCDGRSERNLL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1881
R free: 0.2207
Average B factor: 36.65
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295.15
Crystal growth procedure: 0.2 M Zn acetate
0.1 M imidazole pH 8 
20% PEG 3K
Matthews coefficient: 2.49
Solvent content (%): 50.63
Ligand: 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid (2T1)
Ligand formula: C20 H19 F3 N2 O3
Ligand molecular weight: 392.372
Ligand SMILES: c1ccc(c(c1)C2CCN(CC2)C(=O)Nc3ccccc3C(=O)O)C(F)(F)F
Ligand InChI: InChI=1S/C20H19F3N2O3/c21-20(22,23)16-7-3-1-5-14(16)13-9-11-25(12-10-13)19(28)24-17-8-4-2-6-15(17)18(26)27/h1-8,13H,9-12H2,(H,24,28)(H,26,27)
Release date: 2020-06-03
Crystal structure of the C-terminal Fg domain of TNC with the single FN domain of PTPRZ (PDB entry 8FN8)
Macromolecule: Tenascin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 231 residues
Sequence: GPGSGLLYPFPKDCSQAMLNGDTTSGLYTIYLNGDKAEALEVFCDMTSDGGGWIVFLRRKNGRENFYQNWKAYAAGFGDRREEFWLGLDNLNKITAQGQYELRVDLRDHGETAFAVYDKFSVGDAKTRYKLKVEGYSGTAGDSMAYHNGRSFSTFDKDTDSAITNCALSYKGAFWYRNCHRVNLMGRYGDNNHSQGVNWFHWKGHEHSIQFAEMKLRPSNFRNLEGRRKRA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.164
R free: 0.2053
Average B factor: 26.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% w/v PEG3350, 100 mM Tris-HCl, pH 8.0
Matthews coefficient: 2.03
Solvent content (%): 39.43
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2023-07-12
Thiophenyl-Pyrazolourea Derivatives as Potent, Brian Penetrant, Orally Bioavailable, and Isoform-Selective JNK3 Inhibitors (PDB entry 7KSK)
Macromolecule: Mitogen-activated protein kinase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 464 residues
Sequence: MSLHFLYYCSEPTLDVKIAFCQGFDKQVDVSYIAKHYNMSKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNSEEKTKNGVVKGQPSPSGAAVNSSESLPPSSSVNDISSMSTDQTLASDTDSSLEASAGPLGCCR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.247
R free: 0.29
Average B factor: 50.18
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.2 M ammonium tartrate pH 7.0, 20 % PEG 3350
Matthews coefficient: 1.9
Solvent content (%): 35.17
Ligand: 4-(4-{[(2-chlorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-N-(oxetan-3-yl)thiophene-2-carboxamide (X3V)
Ligand formula: C18 H16 Cl N5 O3 S
Ligand molecular weight: 417.869
Ligand SMILES: c1ccc(c(c1)NC(=O)Nc2cnn(c2)c3cc(sc3)C(=O)NC4COC4)Cl
Ligand InChI: InChI=1S/C18H16ClN5O3S/c19-14-3-1-2-4-15(14)23-18(26)22-11-6-20-24(7-11)13-5-16(28-10-13)17(25)21-12-8-27-9-12/h1-7,10,12H,8-9H2,(H,21,25)(H2,22,23,26)
Release date: 2021-03-03
The crystal structure of upain-1-W3A in complex with uPA at pH9.0 (PDB entry 4ZKR)
Macromolecule: Urokinase-type plasminogen activator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 247 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.36
R work: 0.207
R free: 0.234
Average B factor: 17.51
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 50 mM sodium citrate pH 4.6, 2.0 M ammonium sulfate supplemented with 5% PEG400
Matthews coefficient: 2.16
Solvent content (%): 43.05
Ligand: HEXAETHYLENE GLYCOL (P6G)
Ligand formula: C12 H26 O7
Ligand molecular weight: 282.331
Ligand SMILES: C(COCCOCCOCCOCCOCCO)O
Ligand InChI: InChI=1S/C12H26O7/c13-1-3-15-5-7-17-9-11-19-12-10-18-8-6-16-4-2-14/h13-14H,1-12H2
Release date: 2016-05-18
Human butyrylcholinesterase in complex with decamethonium (PDB entry 6EP4)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 529 residues
Sequence: EDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.30005381157
R work: 0.178719844894
R free: 0.216812272554
Average B factor: 49.960587464
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 MES Buffer, 2.1 M ammonium sulfate
Matthews coefficient: 3.36
Solvent content (%): 63.39
Ligand: DECAMETHONIUM ION (DME)
Ligand formula: C16 H38 N2
Ligand molecular weight: 258.486
Ligand SMILES: C[N+](C)(C)CCCCCCCCCC[N+](C)(C)C
Ligand InChI: InChI=1S/C16H38N2/c1-17(2,3)15-13-11-9-7-8-10-12-14-16-18(4,5)6/h7-16H2,1-6H3/q+2
Release date: 2017-12-13
Crystal structure of BACE1 in complex with aminoquinoline inhibitor 6 (PDB entry 5I3X)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 411 residues
Sequence: LPRETDEEPEEPGKKGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1763
R free: 0.2124
Average B factor: 19.29
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 1.5 M ammonium sulfate, 0.2 M lithium chloride, 0.1 M MES (pH 6.0)
Matthews coefficient: 2.84
Solvent content (%): 56.67
Ligand: N-(1-{3-[2-(2-amino-3-{3-[(3,3-dimethylbutyl)amino]-3-oxopropyl}quinolin-6-yl)phenyl]prop-2-yn-1-yl}cyclopropyl)-4-fluorobenzamide (68J)
Ligand formula: C37 H39 F N4 O2
Ligand molecular weight: 590.73
Ligand SMILES: CC(C)(C)CCNC(=O)CCc1cc2cc(ccc2nc1N)c3ccccc3C#CCC4(CC4)NC(=O)c5ccc(cc5)F
Ligand InChI: InChI=1S/C37H39FN4O2/c1-36(2,3)21-22-40-33(43)17-13-28-24-29-23-27(12-16-32(29)41-34(28)39)31-9-5-4-7-25(31)8-6-18-37(19-20-37)42-35(44)26-10-14-30(38)15-11-26/h4-5,7,9-12,14-16,23-24H,13,17-22H2,1-3H3,(H2,39,41)(H,40,43)(H,42,44)
Release date: 2016-03-30
Crystal structure of human Biliverdin IX-beta reductase B with Ataluren (PTC) (PDB entry 7ERB)
Macromolecule: Flavin reductase (NADPH)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.30
Sequence length: 206 residues
Sequence: MAVKKIAIFGATGQTGLTTLAQAVQAGYEVTVLVRDSSRLPSEGPRPAHVVVGDVLQAADVDKTVAGQDAVIVLLGTRNDLSPTTVMSEGARNIVAAMKAHGVDKVVACTSAFLLWDPTKVPPRLQAVTDDHIRMHKVLRESGLKYVAVMPPHIGDQPLTGAYTVTLDGRGPSRVISKHDLGHFMLRCLTTDEYDGHSTYPSHQYQ
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1708
R free: 0.1986
Average B factor: 20.74
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 1.9-2.0M Ammonium sulfate, 0.1M Bis-tris(pH 6.5)
Matthews coefficient: 2.27
Solvent content (%): 45.73
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: 2022-01-19
Co-crystal structure of PERK with inhibitor (R)-2-amino-N-cyclopropyl-5-(4-(2-(3,5-difluorophenyl)-2-hydroxyacetamido)-2-methylphenyl)nicotinamide (PDB entry 7MF0)
Macromolecule: Eukaryotic translation initiation factor 2-alpha kinase 3,Eukaryotic translation initiation factor 2-alpha kinase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 317 residues
Sequence: GSSSWNDIKNSGYISRYLTDFEPIQCLGRGGFGVVFEAKNKVDDCNYAIKRIRLPNRELAREKVMREVKALAKLEHPGIVRYFNAWLEAPPEKWQEKLQPSSPKVYLYIQMQLCRKENLKDWMNGRCTIEERERSVCLHIFLQIAEAVEFLHSKGLMHRNLKPSNIFFTMDDVVKVGDFGLVTAMDQDEEEQTVLTPMPAYARHTGQVGTKLYMSPEQIHGNSYSHKVDIFSLGLILFELLYPFSTQMERVRTLTDVRNLKFPPLFTQKYPCEYVMVQDMLSPSPMERPEAINIIENAVFEDLDFPGKTVLRQRSRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.809
R work: 0.232
R free: 0.2725
Average B factor: 90.189
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 15% MPD, 10% PEG 8K, 0.1M MgCl2, 0.1M sodium citrate pH 5.6
Matthews coefficient: 2.98
Solvent content (%): 58.76
Ligand: 2-amino-N-cyclopropyl-5-(4-{[(2R)-2-(3,5-difluorophenyl)-2-hydroxyacetyl]amino}-2-methylphenyl)pyridine-3-carboxamide (Z6P)
Ligand formula: C24 H22 F2 N4 O3
Ligand molecular weight: 452.453
Ligand SMILES: Cc1cc(ccc1c2cc(c(nc2)N)C(=O)NC3CC3)NC(=O)C(c4cc(cc(c4)F)F)O
Ligand InChI: InChI=1S/C24H22F2N4O3/c1-12-6-18(30-24(33)21(31)13-7-15(25)10-16(26)8-13)4-5-19(12)14-9-20(22(27)28-11-14)23(32)29-17-2-3-17/h4-11,17,21,31H,2-3H2,1H3,(H2,27,28)(H,29,32)(H,30,33)/t21-/m1/s1
Release date: 2021-05-19
Crystal Structure of Factor VIIa in complex with 1-(2,6-difluorophenyl)-3-[[3-[5-hydroxy-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-1-yl]phenyl]methyl]urea (PDB entry 5PAX)
Macromolecule: Coagulation factor VII heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 254 residues
Sequence: IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.36
R work: 0.1816
R free: 0.1916
Average B factor: 16.897
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol
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: 2017-06-21
Human Ornithine Aminotransferase (hOAT) crystallized at pH 6.0 (PDB entry 7T9Z)
Macromolecule: Ornithine aminotransferase, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.6.1.13
Sequence length: 439 residues
Sequence: MFSKLAHLQRFAVLSRGVHSSVASATSVATKKTVQGPPTSDDIFEREYKYGAHNYHPLPVALERGKGIYLWDVEGRKYFDFLSSYSAVNQGHCHPKIVNALKSQVDKLTLTSRAFYNNVLGEYEEYITKLFNYHKVLPMNTGVEAGETACKLARKWGYTVKGIQKYKAKIVFAAGNFWGRTLSAISSSTDPTSYDGFGPFMPGFDIIPYNDLPALERALQDPNVAAFMVEPIQGEAGVVVPDPGYLMGVRELCTRHQVLFIADEIQTGLARTGRWLAVDYENVRPDIVLLGKALSGGLYPVSAVLCDDDIMLTIKPGEHGSTYGGNPLGCRVAIAALEVLEEENLAENADKLGIILRNELMKLPSDVVTAVRGKGLLNAIVIKETKDWDAWKVCLRLRDNGLLAKPTHGDIIRFAPPLVIKEDELRESIEIINKTILSF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.2656
R free: 0.2759
Average B factor: 23.88
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: Purified holo-hOAT was buffer-exchanged into 100 mM MES, 200 mM NaCl, 100 uM PLP, pH 6.0 buffer, and then concentrated to ~6 mg/mL. The crystallization was performed via the hanging drop vapor diffusion method according to previously published conditions with 50 mM Tricine pH 7.8 substituted to 50 mM MES pH 6.0 buffer. The crystals grew at room temperature within three days and reached their maximum size in a week.
Matthews coefficient: 2.09
Solvent content (%): 41.03
Ligand: PYRIDOXAL-5'-PHOSPHATE (PLP)
Ligand formula: C8 H10 N O6 P
Ligand molecular weight: 247.142
Ligand SMILES: Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
Ligand InChI: InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
Release date: 2022-05-04
ERK5 in complex with small molecule (PDB entry 5BYZ)
Macromolecule: Mitogen-activated protein kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 348 residues
Sequence: TFDVGDEYEIIETIGNGAYGVVSSARRRLTGQQVAIKKIPNAFDVVTNAKRTLRELKILKHFKHDNIIAIKDILRPTVPYGEFKSVYVVLDLMESDLHQIIHSSQPLTLEHVRYFLYQLLRGLKYMHSAQVIHRDLKPSNLLVNENCELKIGDFGMARGLCTSPAEHQYFMTEYVATRWYRAPELMLSLHEYTQAIDLWSVGCIFGEMLARRQLFPGKNYVHQLQLIMMVLGTPSPAVIQAVGAERVRAYIQSLPPRQPVPWETVYPGADRQALSLLGRMLRFEPSARISAAAALRHPFLAKYHDPDDEPDCAPPFDFAFDREALTRERIKEAIVAEIEDFHARREGI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.17367
R free: 0.19225
Average B factor: 17.515
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 11 % PEG4000
0.01 M MgCl2
0.18 M Na-Formiate
0.10 M MES, pH=6.50
0.01 M Tris/Cl, pH=8.50
Matthews coefficient: 3.24
Solvent content (%): 62.05
Ligand: 4-({5-fluoro-4-[2-methyl-1-(propan-2-yl)-1H-imidazol-5-yl]pyrimidin-2-yl}amino)-N-[2-(piperidin-1-yl)ethyl]benzamide (4WE)
Ligand formula: C25 H32 F N7 O
Ligand molecular weight: 465.566
Ligand SMILES: Cc1ncc(n1C(C)C)c2c(cnc(n2)Nc3ccc(cc3)C(=O)NCCN4CCCCC4)F
Ligand InChI: InChI=1S/C25H32FN7O/c1-17(2)33-18(3)28-16-22(33)23-21(26)15-29-25(31-23)30-20-9-7-19(8-10-20)24(34)27-11-14-32-12-5-4-6-13-32/h7-10,15-17H,4-6,11-14H2,1-3H3,(H,27,34)(H,29,30,31)
Release date: 2016-05-04
Human SIRT3 Recognizing H3K4cr (PDB entry 6ISO)
Macromolecule: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 275 residues
Sequence: GKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.22144
R free: 0.27519
Average B factor: 47.693
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 12% PEG4K, 0.1 M sodium malonate, pH 6.5, 5% isopropanol
Matthews coefficient: 2.85
Solvent content (%): 60.85
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2019-01-23
The ligand-free structure of human PPARgamma ligand-binding domain R288A mutant in the presence of the SRC-1 coactivator peptide (PDB entry 6KTM)
Macromolecule: Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 283 residues
Sequence: AEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFASVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2166
R free: 0.2575
Average B factor: 72.077
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 296
Crystal growth procedure: 2.2 M sodium malonate (pH 7.0)
Matthews coefficient: 2.72
Solvent content (%): 54.9
Release date: 2020-02-05