satarupa22/MacromolecularLigandDB huggingface dataset:
LTA4 hydrolase in complex with fragment2 (PDB entry 7AV1)
Macromolecule: Leukotriene A-4 hydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 613 residues
Sequence: GPGPEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPDVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1567
R free: 0.1957
Average B factor: 22.41
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 8000, 0.1 IMIDAZOLE PH 6.8, 0.1 SODIUM ACETATE, 0.005 M YBCL3
Matthews coefficient: 2.42
Solvent content (%): 49.1
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2021-02-17
Crystal structure of the SHOC2-MRAS-PP1CA (SMP) complex to a resolution of 2.17 Angstrom (PDB entry 7TVF)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 329 residues
Sequence: SDSEKLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPADKNKGKYGQFSGLNPGGRPITPPRNSAKAKK
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.1988
R free: 0.2259
Average B factor: 52.4903
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: Crystals originally grown in 15% PEG 1500, 0.1M MIB pH 4.2 (15mg/ml of SMP) were used to make seeds. Microseeded into a condition with a reservoir consisting of 17.8% PEG 3350, 136mM sodium sulfate with 1:10 dilution of seeds (7.5mg/ml of SMP) using a ratio of 200nl protein:133nl reservoir:67nl diluted seeds
Matthews coefficient: 2.81
Solvent content (%): 56.22
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: 2022-05-04
Carbonic anhydrase inhibitors: Design and synthesis of new heteroaryl-N-carbonylbenzenesulfonamides targeting druggable human carbonic anhydrase isoforms (hCA VII, hCA IX, and hCA XIV) (PDB entry 4Z1N)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 258 residues
Sequence: HHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47
R work: 0.1886
R free: 0.2138
Average B factor: 10.329
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 50mM Tris-HCl, 1,6 M Sodium Citrate
Matthews coefficient: 2.1
Solvent content (%): 41.45
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: 2015-08-26
The phosphatase and C2 domains of SHIP1 with covalent Z56948267 (PDB entry 8PDJ)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1326
R free: 0.1898
Average B factor: 21.222
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM MES/imidazole 20 % PEG 500 MME, 10% PEG 20,000
Matthews coefficient: 2.11
Solvent content (%): 41.83
Ligand: 4-azanyl-3-fluoranyl-benzenethiol (YC5)
Ligand formula: C6 H6 F N S
Ligand molecular weight: 143.182
Ligand SMILES: c1cc(c(cc1S)F)N
Ligand InChI: InChI=1S/C6H6FNS/c7-5-3-4(9)1-2-6(5)8/h1-3,9H,8H2
Release date: 2023-06-28
PRMT5:MEP50 Complexed with 5,5-Bicyclic Inhibitor Compound 4 (PDB entry 7KIB)
Macromolecule: Methylosome protein 50
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 350 residues
Sequence: MHHHHHHHHRKETPPPLVPPAAREWNLPPNAPACMERQLEAARYRSDGALLLGASSLSGRCWAGSLWLFKDPCAAPNEGFCSAGVQTEAGVADLTWVGERGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDICIKVWDLAQQVVLSSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQIGCSAPGYLPTSLAWHPQQSEVFVFGDENGTVSLVDTKSTSCVLSSAVHSQCVTGLVFSPHSVPFLASLSEDCSLAVLDSSLSELFRSQAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHVVPTEPLPAPGPASVTE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.193
R free: 0.245
Average B factor: 66.74
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M sodium citrate pH 6.0, 0.2 M sodium acetate, 10-12% PEG 4000
Matthews coefficient: 2.86
Solvent content (%): 57.06
Ligand: (2R,3R,3aS,6S,6aR)-6-[(2-amino-3-bromoquinolin-7-yl)oxy]-2-(4-amino-7H-pyrrolo[2,3-d]pyrimidin-7-yl)hexahydro-3aH-cyclopenta[b]furan-3,3a-diol (WFM)
Ligand formula: C22 H21 Br N6 O4
Ligand molecular weight: 513.344
Ligand SMILES: c1cc(cc2c1cc(c(n2)N)Br)OC3CCC4(C3OC(C4O)n5ccc6c5ncnc6N)O
Ligand InChI: InChI=1S/C22H21BrN6O4/c23-13-7-10-1-2-11(8-14(10)28-19(13)25)32-15-3-5-22(31)16(30)21(33-17(15)22)29-6-4-12-18(24)26-9-27-20(12)29/h1-2,4,6-9,15-17,21,30-31H,3,5H2,(H2,25,28)(H2,24,26,27)/t15-,16-,17+,21+,22-/m0/s1
Release date: 2021-04-21
Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser448 (PDB entry 6ZC9)
Macromolecule: 14-3-3 protein gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 234 residues
Sequence: MVDREQLVQKARLAEQAERYDDMAAAMKNVTELNEPLSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTSADGNEKKIEMVRAYREKIEKELEAVCQDVLSLLDNYLIKNCSETQYESKVFYLKMKGDYYRYLAEVATGEKRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALNYSVFYYEIQNAPEQACHLAKTAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWT
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89895988606
R work: 0.211915834691
R free: 0.239347564833
Average B factor: 44.8045996391
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293.15
Crystal growth procedure: PEG 400, magnesium chloride, HEPES, hexafluoro-2-propanol
Matthews coefficient: 2.7
Solvent content (%): 54.47
Ligand: 1,1,1,3,3,3-hexafluoropropan-2-ol (CFH)
Ligand formula: C3 H2 F6 O
Ligand molecular weight: 168.038
Ligand SMILES: C(C(F)(F)F)(C(F)(F)F)O
Ligand InChI: InChI=1S/C3H2F6O/c4-2(5,6)1(10)3(7,8)9/h1,10H
Release date: 2021-07-21
CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-40 A.K.A 7-[(1R)-1-phenyl-3-{[(1r,4r)-4-phenylcyclohexyl]amino}propyl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine (PDB entry 6WY0)
Macromolecule: Myeloperoxidase light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.2.2
Sequence length: 105 residues
Sequence: CPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPAA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.799
R work: 0.1846
R free: 0.2162
Average B factor: 55.74
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 0.1M Hepes pH 7.5, 150mM NaCl, 20-25%(V/V)PEG3350.Crystals were cryoprotected by supplementing the mother liquor with 15% (v/v) ethylene glycol and harvested by flash-cooling in liquid nitrogen
Matthews coefficient: 2.43
Solvent content (%): 49.29
Ligand: HEME C (HEC)
Ligand formula: C34 H34 Fe N4 O4
Ligand molecular weight: 618.503
Ligand SMILES: CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
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,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
Release date: 2020-10-14
Tankyrase 2 in complex with an inhibitor (OM-1700) (PDB entry 6TG4)
Macromolecule: Tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 240 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.76
R work: 0.2296
R free: 0.2809
Average B factor: 44.877
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295.15
Crystal growth procedure: 7.5-25% PEG 6000, Bicine, pH = 9.0
Matthews coefficient: 2.28
Solvent content (%): 45.96
Ligand: ~{N}-[3-[5-(5-ethoxypyridin-2-yl)-4-(2-fluorophenyl)-1,2,4-triazol-3-yl]cyclobutyl]pyridine-2-carboxamide (N8K)
Ligand formula: C25 H23 F N6 O2
Ligand molecular weight: 458.488
Ligand SMILES: CCOc1ccc(nc1)c2nnc(n2c3ccccc3F)C4CC(C4)NC(=O)c5ccccn5
Ligand InChI: InChI=1S/C25H23FN6O2/c1-2-34-18-10-11-20(28-15-18)24-31-30-23(32(24)22-9-4-3-7-19(22)26)16-13-17(14-16)29-25(33)21-8-5-6-12-27-21/h3-12,15-17H,2,13-14H2,1H3,(H,29,33)/t16-,17-
Release date: 2020-07-08
Crystal Structure of human cyclic GMP-AMP synthase in complex with 6-(2-chloro-4-methylphenyl)-2-(morpholin-4-ylmethyl)-1H-benzimidazole-4-carboxylic acid (PDB entry 7FUC)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.253
R free: 0.291
Average B factor: 123.42
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals
Matthews coefficient: 2.56
Solvent content (%): 51.86
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: 2024-02-21
Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor (S)-2-(((1r,4S)-4-(4-amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclohexyl)amino)-4-methylpentanoic acid (PDB entry 5H0B)
Macromolecule: Tyrosine-protein kinase HCK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 454 residues
Sequence: GAMGSGIRIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLETEEWFFKGISRKDAERQLLAPGNMLGSFMIRDSETTKGSYSLSVRDYDPRQGDTVKHYKIRTLDNGGFYISPRSTFSTLQELVDHYKKGNDGLCQKLSVPCMSSKPQKPWEKDAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPGSMSVEAFLAEANVMKTLQHDKLVKLHAVVTKEPIYIITEFMAKGSLLDFLKSDEGSKQPLPKLIDFSAQIAEGMAFIEQRNYIHRDLRAANILVSASLVCKIADFGLARVIEDNEYTAREGAKFPIKWTAPEAINFGSFTIKSDVWSFGILLMEIVTYGRIPYPGMSNPEVIRALERGYRMPRPENCPEELYNIMMRCWKNRPEERPTFEYIQSVLDDFYTATESQYEEIP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.651
R work: 0.1802
R free: 0.2049
Average B factor: 38.4663
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.22-0.25 M ammonium formate, 12-22 % PEG 3350
Matthews coefficient: 2.34
Solvent content (%): 47.44
Ligand: (2~{S})-2-[[4-[4-azanyl-5-(4-phenoxyphenyl)pyrrolo[2,3-d]pyrimidin-7-yl]cyclohexyl]azaniumyl]-4-methyl-pentanoate (OOQ)
Ligand formula: C30 H35 N5 O3
Ligand molecular weight: 513.631
Ligand SMILES: CC(C)CC(C(=O)[O-])[NH2+]C1CCC(CC1)n2cc(c3c2ncnc3N)c4ccc(cc4)Oc5ccccc5
Ligand InChI: InChI=1S/C30H35N5O3/c1-19(2)16-26(30(36)37)34-21-10-12-22(13-11-21)35-17-25(27-28(31)32-18-33-29(27)35)20-8-14-24(15-9-20)38-23-6-4-3-5-7-23/h3-9,14-15,17-19,21-22,26,34H,10-13,16H2,1-2H3,(H,36,37)(H2,31,32,33)/t21-,22+,26-/m0/s1
Release date: 2017-10-11
The RYK Pseudokinase Domain (PDB entry 6TUA)
Macromolecule: Tyrosine-protein kinase RYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 317 residues
Sequence: SITSSLGYPTLRIEKNDLRSVTLLEAKGKVKDIAISRERITLKDVLQEGTFGRIFHGILIDEKDPNKEKQAFVKTVKDQASEIQVTMMLTESCKLRGLHHRNLLPITHVCIEEGEKPMVILPYMNWGNLKLFLRQCKLVEANNPQAISQQDLVHMAIQIACGMSYLARREVIHKDLAARNCVIDDTLQVKITDNALSRDLFPMDYHCLGDNENRPVRWMALESLVNNEFSSASDVWAFGVTLWELMTLGQTPYVDIDPFEMAAYLKDGYRIAQPINCPDELFAVMACCWALDPEERPKFQQLVQCLTEFHAALGAYV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.1937
R free: 0.2476
Average B factor: 40.74
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.5 M lithium sulfate, 0.1 M HEPES 7.5
Matthews coefficient: 3
Solvent content (%): 59.06
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: 2020-01-15
Human PRMT5:MEP50 structure with Fragment 4 and MTA Bound (PDB entry 7UYF)
Macromolecule: Protein arginine N-methyltransferase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.320
Sequence length: 645 residues
Sequence: MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.82
R work: 0.2688
R free: 0.3149
Average B factor: 33.215
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 281
Crystal growth procedure: 10% PEG 4000, 100 mM Sodium Acetate, 100 mM Sodium Citrate pH 5.4
Matthews coefficient: 2.95
Solvent content (%): 58.26
Ligand: 4-methyl-1,5-naphthyridin-2-amine (PUI)
Ligand formula: C9 H9 N3
Ligand molecular weight: 159.188
Ligand SMILES: Cc1cc(nc2c1nccc2)N
Ligand InChI: InChI=1S/C9H9N3/c1-6-5-8(10)12-7-3-2-4-11-9(6)7/h2-5H,1H3,(H2,10,12)
Release date: 2022-10-05
Crystal structure of apo PTP1B D181A/Q262A phosphatase domain (PDB entry 8EXI)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 298 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHEEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPAFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIATADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.599
R work: 0.1911
R free: 0.2139
Average B factor: 31.7486
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281.15
Crystal growth procedure: 12% PEG 8K, 0.15 M Magnesium Acetate, 0.1 M MES (pH 6.5)
Matthews coefficient: 3.44
Solvent content (%): 64.23
Ligand: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID (MES)
Ligand formula: C6 H13 N O4 S
Ligand molecular weight: 195.237
Ligand SMILES: C1COCC[NH+]1CCS(=O)(=O)[O-]
Ligand InChI: InChI=1S/C6H13NO4S/c8-12(9,10)6-3-7-1-4-11-5-2-7/h1-6H2,(H,8,9,10)
Release date: 2023-07-05
Crystal structure of MerTK Kinase domain with BMS794833 (PDB entry 7XHY)
Macromolecule: Tyrosine-protein kinase Mer
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 298 residues
Sequence: GSHMEELQNKLEDVVIDRNLLILGRILGEGEFGSVMEGNLKQEDGTSLKVAVKTMKLDNSSQREIEEFLSEAACMKDFSHPNVIRLLGVCIEMSSQGIPKPMVILPFMKYGDLHTYLLYSRLETGPRHIPLQTLLRFMVDIALGMEYLSNRNFLHRDLAARNCMLRDDMTVCVADFGLSKKIYSGDYYRQGRIAKMPVKWIAIESLADRVYTSKSDVWAFGVTMWEIATRGMTPYPGVQNHEMYDYLLHGHRLKQPEDCLDELYEIMYSCWRTDPLDRPTFSVLRLQLERLLESLPDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.16
R work: 0.208
R free: 0.2523
Average B factor: 47.47
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 287
Crystal growth procedure: Protein concentration 25 mg/mL

Protein storage buffer: 
Tris-HCl pH 8.0, 500 mM NaCl, 1 mM Tris(2-carboxyethyl)phosphine Hydrochloride (TCEP)

Mother Liquor: 0.1 M Tris-HCl pH 8.5, 4.3 M NaCl

Protein: Reservoir: Apo-Microseed = 300: 300: 100 nL or 400: 400: 100 nL 

Co-crystalization
2mM compound preincubation: 2Hours in ICE

Cryoprotectant solution:
0.1 M Tris-HCl pH 8.5, 2.5 M NaCl, 20% DMSO, 10 mM compounds
Matthews coefficient: 2.11
Solvent content (%): 41.82
Ligand: ~{N}-[4-(2-azanyl-3-chloranyl-pyridin-4-yl)oxy-3-fluoranyl-phenyl]-5-(4-fluorophenyl)-4-oxidanylidene-1~{H}-pyridine-3-carboxamide (E0X)
Ligand formula: C23 H15 Cl F2 N4 O3
Ligand molecular weight: 468.84
Ligand SMILES: c1cc(ccc1C2=CNC=C(C2=O)C(=O)Nc3ccc(c(c3)F)Oc4ccnc(c4Cl)N)F
Ligand InChI: InChI=1S/C23H15ClF2N4O3/c24-20-19(7-8-29-22(20)27)33-18-6-5-14(9-17(18)26)30-23(32)16-11-28-10-15(21(16)31)12-1-3-13(25)4-2-12/h1-11H,(H2,27,29)(H,28,31)(H,30,32)
Release date: 2022-11-30
Structure of Compound 6 Bound to CK2alpha (PDB entry 7ZYD)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.404
R work: 0.1979
R free: 0.2139
Average B factor: 26.12
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.04
Solvent content (%): 39.63
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: 2022-10-12
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with PCM-0102253-001 (PDB entry 7G9I)
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): 2.202
R work: 0.2122
R free: 0.2738
Average B factor: 50.83
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: 2.46
Solvent content (%): 50.04
Ligand: N-[(2-methylphenyl)methyl]acetamide (ZGQ)
Ligand formula: C10 H13 N O
Ligand molecular weight: 163.216
Ligand SMILES: Cc1ccccc1CNC(=O)C
Ligand InChI: InChI=1S/C10H13NO/c1-8-5-3-4-6-10(8)7-11-9(2)12/h3-6H,7H2,1-2H3,(H,11,12)
Release date: 2023-07-12
Crystal structure of TTBK2 in complex with VNG1.33 (compound 27) (PDB entry 7Q8Z)
Macromolecule: Tau-tubulin kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 300 residues
Sequence: SMSGGGEQPDILSVGILVKERWKVLRKIGGGGFGEIYDALDMLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNDRFNYVVMQLQGRNLADLRRSQSRGTFTISTTLRLGRQILESIESIHSVGFLHRDIKPSNFAMGRFPSTCRKCYMLDFGLARQFTNSCGDVRPPRAVAGFRGTVRYASINAHRNREMGRHDDLWSLFYMLVEFVVGQLPWRKIKDKEQVGSIKERYDHRLMLKHLPPEFSIFLDHISSLDYFTKPDYQLLTSVFDNSIKTFGVIESDPFDWEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1749
R free: 0.2033
Average B factor: 22.032
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 1.6M Na/K phosphate pH 7, 5% Glycerol, 0.1M tris 8.5
Matthews coefficient: 2.81
Solvent content (%): 56.15
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2022-03-09