satarupa22/MacromolecularLigandDB huggingface dataset:
Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors: tert-butyl [(2S)-1-{[(3S,17S)-2,16-dioxo-10,15-dioxa-1,21-diazatricyclo[15.3.1.1~5,9~]docosa-5(22),6,8-trien-3-yl]amino}-3-methyl-1-oxobutan-2-yl]carbamate (compound 3) (PDB entry 6X4M)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 167 residues
Sequence: GHMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1524
R free: 0.1713
Average B factor: 13.56
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG3350, 5% ethanol
Matthews coefficient: 2.73
Solvent content (%): 54.91
Ligand: tert-butyl [(2S)-1-{[(3S,17S)-2,16-dioxo-10,15-dioxa-1,21-diazatricyclo[15.3.1.1~5,9~]docosa-5(22),6,8-trien-3-yl]amino}-3-methyl-1-oxobutan-2-yl]carbamate (UMM)
Ligand formula: C28 H42 N4 O7
Ligand molecular weight: 546.656
Ligand SMILES: CC(C)C(C(=O)NC1Cc2cccc(c2)OCCCCOC(=O)C3CCCN(C1=O)N3)NC(=O)OC(C)(C)C
Ligand InChI: InChI=1S/C28H42N4O7/c1-18(2)23(30-27(36)39-28(3,4)5)24(33)29-22-17-19-10-8-11-20(16-19)37-14-6-7-15-38-26(35)21-12-9-13-32(31-21)25(22)34/h8,10-11,16,18,21-23,31H,6-7,9,12-15,17H2,1-5H3,(H,29,33)(H,30,36)/t21-,22-,23-/m0/s1
Release date: 2020-06-24
Human LSD1/CoREST bound to the quinazoline inhibitor MC4106 (PDB entry 6TUY)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 853 residues
Sequence: MLSGKKAAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERTPRKKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGRRTSRRKRAKVEYREMDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAPPEEENESEPEEPSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTLPRQATPGVPAQQSPSMP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2039
R free: 0.2229
Average B factor: 80.525
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 20 degrees  C in 100 mM N-(2-
acetamido)iminodiacetic acid (pH 6.5) and 1.2 M Na-K tartrate
Matthews coefficient: 4.29
Solvent content (%): 71.3
Ligand: ~{N}2-[3-(dimethylamino)propyl]-6,7-dimethoxy-~{N}4-[1-(naphthalen-2-ylmethyl)piperidin-4-yl]quinazoline-2,4-diamine (NY8)
Ligand formula: C31 H40 N6 O2
Ligand molecular weight: 528.688
Ligand SMILES: CN(C)CCCNc1nc2cc(c(cc2c(n1)NC3CCN(CC3)Cc4ccc5ccccc5c4)OC)OC
Ligand InChI: InChI=1S/C31H40N6O2/c1-36(2)15-7-14-32-31-34-27-20-29(39-4)28(38-3)19-26(27)30(35-31)33-25-12-16-37(17-13-25)21-22-10-11-23-8-5-6-9-24(23)18-22/h5-6,8-11,18-20,25H,7,12-17,21H2,1-4H3,(H2,32,33,34,35)
Release date: 2021-07-21
Crystal structure of human tryptophan hydroxylase 1 in complex with inhibitor LP533401 (PDB entry 7ZIK)
Macromolecule: Tryptophan 5-hydroxylase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.16.4
Sequence length: 326 residues
Sequence: MKHHHHHHHGAAGTSLYKKAGENLYFQGSVPWFPKKISDLDHCANRVLMYGSELDADHPGFKDNVYRKRRKYFADLAMNYKHGDPIPKVEFTEEEIKTWGTVFQELNKLYPTHACREYLKNLPLLSKYCGYREDNIPQLEDVSNFLKERTGFSIRPVAGYLSPRDFLSGLAFRVFHCTQYVRHSSDPFYTPEPDTCHELLGHVPLLAEPSFAQFSQEIGLASLGASEEAVQKLATCYFFTVEFGLCKQDGQLRVFGAGLLSSISELKHALSGHAKVKPFDPKITCKQECLITTFQDVYFVSESFEDAKEKMREFTKTIKRPFGVKY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58925907124
R work: 0.223576011016
R free: 0.259070423425
Average B factor: 37.9885529752
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 27% w/v PEG 3350, 0.1 M Bis-Tris pH 6.5
Matthews coefficient: 2.16
Solvent content (%): 42.93
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2022-09-07
Synaptic complex of human DNA polymerase Lambda DL variant engaged on a DNA double-strand break containing an unpaired 3' primer terminus (PDB entry 8U0O)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 341 residues
Sequence: GSAAAVLDKWVCAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2148
R free: 0.2586
Average B factor: 58.81
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 294
Crystal growth procedure: 0.1 M ADA pH 6.5, 1 M ammonium phosphate dibasic
Matthews coefficient: 2.48
Solvent content (%): 50.35
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2024-03-13
STRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN BOUND TETHERED WITH SRC co-activator peptide IN COMPLEX WITH (S,S)-1 (PDB entry 6XP9)
Macromolecule: Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1 fusion
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 351 residues
Sequence: HHHHHHGSERTGTQPLGVQGLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGITGSSGGSGGSSHSSLTERHKILHRLLQEGSPSDITTLSVEPD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.27
R work: 0.1949
R free: 0.2199
Average B factor: 60.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 0.1 M Ammonium acetate, 0.1 M Sodium HEPES pH 7.5, 18-20 % w/v PEG 4000.Crystals were cryoprotected by supplementing the mother liquor with 20% (v/v) Glycerol and harvested by flash-cooling in liquid nitrogen
Matthews coefficient: 2.5
Solvent content (%): 50.78
Ligand: (2S)-tert-butoxy[7-(8-fluoro-5-methyl-3,4-dihydro-2H-1-benzopyran-6-yl)-5-methyl-2-phenylpyrazolo[1,5-a]pyrimidin-6-yl]acetic acid (QCG)
Ligand formula: C29 H30 F N3 O4
Ligand molecular weight: 503.565
Ligand SMILES: Cc1c(cc(c2c1CCCO2)F)c3c(c(nc4n3nc(c4)c5ccccc5)C)C(C(=O)O)OC(C)(C)C
Ligand InChI: InChI=1S/C29H30FN3O4/c1-16-19-12-9-13-36-26(19)21(30)14-20(16)25-24(27(28(34)35)37-29(3,4)5)17(2)31-23-15-22(32-33(23)25)18-10-7-6-8-11-18/h6-8,10-11,14-15,27H,9,12-13H2,1-5H3,(H,34,35)/t27-/m0/s1
Release date: 2020-09-23
Human DNA polymerase eta R61A-DNA ternary complex: reaction with 1 mM Mg2+ for 80s (PDB entry 5KFU)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTASMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.181
R free: 0.211
Average B factor: 23.74
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 17% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.09
Solvent content (%): 41.21
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: 2016-06-22
Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe (PDB entry 5DKD)
Macromolecule: Transcription activator BRG1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4
Sequence length: 121 residues
Sequence: SMLSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKEDD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.26773
R free: 0.29729
Average B factor: 32.2
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M Bis Tris pH 7.2, 0.1 M ammonium acetate, 0.1 M ZnCl2, 15% PEG smear high (mixture from PEG8k to 20k)
Matthews coefficient: 2.98
Solvent content (%): 58.78
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: 2015-10-14
Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant at pH 5.0 (PDB entry 7A2S)
Macromolecule: Tyrosine-protein kinase Fyn
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 62 residues
Sequence: GGVTLFVALYDYEARTEDDLSFHKGEKFQIVNNTEGDWWLAHSLTTGETGYIPSNYVAPVDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.02
R work: 0.1593
R free: 0.1748
Average B factor: 12.53
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 298
Crystal growth procedure: 2.0 ammonium sulfate, 0.1M sodium acetate
Matthews coefficient: 1.98
Solvent content (%): 37.78
Release date: 2021-08-25
HUMAN PRMT5:MEP50 COMPLEX WITH MTA and Fragment 5 Bound (PDB entry 7UY1)
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): 2.66
R work: 0.26
R free: 0.3
Average B factor: 52
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 291
Crystal growth procedure: PEG/Buffer/Salt
Matthews coefficient: 2.97
Solvent content (%): 58.58
Ligand: 3-methyl-1,5-naphthyridin-2-amine (PJ0)
Ligand formula: C9 H9 N3
Ligand molecular weight: 159.188
Ligand SMILES: Cc1cc2c(cccn2)nc1N
Ligand InChI: InChI=1S/C9H9N3/c1-6-5-8-7(12-9(6)10)3-2-4-11-8/h2-5H,1H3,(H2,10,12)
Release date: 2022-10-05
CDK1/Cks2 in complex with Dinaciclib (PDB entry 6GU6)
Macromolecule: Cyclin-dependent kinases regulatory subunit 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 84 residues
Sequence: GPLGSMAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFRRPLPKDQQK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.20092
R free: 0.24586
Average B factor: 47.498
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: CONDITIONS AROUND 0.1M BIS-TRIS(PH6.5), 0.2M SODIUM NITRATE 20% PEG3350, PROTEIN AT 10-12 MG/ML, 0.5Mm INHIBITOR
Matthews coefficient: 2.76
Solvent content (%): 55.39
Ligand: 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium (1QK)
Ligand formula: C21 H29 N6 O2
Ligand molecular weight: 397.494
Ligand SMILES: CCc1cnn2c1nc(cc2NCc3ccc[n+](c3)O)N4CCCCC4CCO
Ligand InChI: InChI=1S/C21H29N6O2/c1-2-17-14-23-27-19(22-13-16-6-5-9-25(29)15-16)12-20(24-21(17)27)26-10-4-3-7-18(26)8-11-28/h5-6,9,12,14-15,18,22,28-29H,2-4,7-8,10-11,13H2,1H3/q+1/t18-/m0/s1
Release date: 2018-12-05
CRYSTAL STRUCTURE OF RAR-RELATED ORPHAN RECEPTOR C (NHIS- RORGT(244-487)-L6-SRC1(678-692)) IN COMPLEX WITH A TRICYCLIC INVERSE AGONIST (PDB entry 6U25)
Macromolecule: NUCLEAR RECEPTOR COACTIVATOR 1 CHIMERA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 285 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLYKELFSTSGGSGGLTERHKILHRLLQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.61
R work: 0.206
R free: 0.247
Average B factor: 58.1
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 20-26% PEG3350, 0.2 M MAGNESIUM          CHLORIDE, 0.1 M BIS-TRIS PH 5.5-6.5
Matthews coefficient: 2.29
Solvent content (%): 46.21
Ligand: trans-4-[(3aR,9bR)-9b-[(4-fluorophenyl)sulfonyl]-7-(1,1,1,2,3,3,3-heptafluoropropan-2-yl)-1,2,3a,4,5,9b-hexahydro-3H-benzo[e]indole-3-carbonyl]cyclohexane-1-carboxylic acid (O5B)
Ligand formula: C29 H27 F8 N O5 S
Ligand molecular weight: 653.581
Ligand SMILES: c1cc(ccc1F)S(=O)(=O)C23CCN(C2CCc4c3ccc(c4)C(C(F)(F)F)(C(F)(F)F)F)C(=O)C5CCC(CC5)C(=O)O
Ligand InChI: InChI=1S/C29H27F8NO5S/c30-20-7-9-21(10-8-20)44(42,43)26-13-14-38(24(39)16-1-3-17(4-2-16)25(40)41)23(26)12-5-18-15-19(6-11-22(18)26)27(31,28(32,33)34)29(35,36)37/h6-11,15-17,23H,1-5,12-14H2,(H,40,41)/t16-,17-,23-,26-/m1/s1
Release date: 2019-11-06
The strucuture of Compound 15 bound to CK2alpha (PDB entry 8AE7)
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): 1.28
R work: 0.204
R free: 0.2317
Average B factor: 20.2
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.03
Solvent content (%): 39.49
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: 2023-03-29
ATAD2 in complex with FragLite23 (PDB entry 7QYL)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.22
R free: 0.2437
Average B factor: 33.702
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
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: 2022-11-23
Human carbonic anhydrase II in complex with 2,3,5,6-tetrafluoro-N-methyl-4-propylsulfanyl-benzenesulfonamide (PDB entry 7AES)
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): 1.4
R work: 0.17
R free: 0.2091
Average B factor: 21.161
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M sodium bicine (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7)
Matthews coefficient: 2.05
Solvent content (%): 40.13
Ligand: 2,3,5,6-tetrakis(fluoranyl)-~{N}-methyl-4-propylsulfanyl-benzenesulfonamide (R8Q)
Ligand formula: C10 H11 F4 N O2 S2
Ligand molecular weight: 317.323
Ligand SMILES: CCCSc1c(c(c(c(c1F)F)S(=O)(=O)NC)F)F
Ligand InChI: InChI=1S/C10H11F4NO2S2/c1-3-4-18-9-5(11)7(13)10(8(14)6(9)12)19(16,17)15-2/h15H,3-4H2,1-2H3
Release date: 2021-09-01
Crystal structure of c-MET bound by compound 3 (PDB entry 7B3V)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 299 residues
Sequence: GNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.225
R free: 0.248
Average B factor: 28.99
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 273
Crystal growth procedure: 25 % PEG3350, 0.2 M (NH4)2SO4, PCPT pH 5.5
Matthews coefficient: 2.6
Solvent content (%): 52.73
Ligand: 3-(3-methyl-1~{H}-pyrrolo[2,3-b]pyridin-5-yl)-1~{H}-pyrrolo[3,4-b]pyrrol-6-one (SWB)
Ligand formula: C14 H12 N4 O
Ligand molecular weight: 252.271
Ligand SMILES: Cc1c[nH]c2c1cc(cn2)c3c[nH]c4c3CNC4=O
Ligand InChI: InChI=1S/C14H12N4O/c1-7-3-16-13-9(7)2-8(4-17-13)10-5-15-12-11(10)6-18-14(12)19/h2-5,15H,6H2,1H3,(H,16,17)(H,18,19)
Release date: 2020-12-09
Structure of cyclophilin A in complex with 3-chloropyridin-2-amine (PDB entry 5NOQ)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.16525
R free: 0.19617
Average B factor: 19.348
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 279.15
Crystal growth procedure: PEG 8000, Tris-HCl
Matthews coefficient: 2.71
Solvent content (%): 54.55
Ligand: 3-chloranylpyridin-2-amine (93E)
Ligand formula: C5 H5 Cl N2
Ligand molecular weight: 128.56
Ligand SMILES: c1cc(c(nc1)N)Cl
Ligand InChI: InChI=1S/C5H5ClN2/c6-4-2-1-3-8-5(4)7/h1-3H,(H2,7,8)
Release date: 2017-07-12
Crystal structure of TNIK-thiopeptide wTP3 complex (PDB entry 8WM0)
Macromolecule: TRAF2 and NCK-interacting protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 306 residues
Sequence: GPDEIDLSALRDPAGIFELVELVGNGTYGQVYKGRHVKTGQLAAIKVMDVTGDEEEEIKQEINMLKKYSHHRNIATYYGAFIKKNPPGMDDQLWLVMEFCGAGSVTDLIKNTKGNTLKEEWIAYICREILRGLSHLHQHKVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATYDFKSDLWSLGITAIEMAEGAPPLCDMHPMRALFLIPRNPAPRLKSKKWSKKFQSFIESCLVKNHSQRPATEQLMKHPFIRDQPNERQVRIQLKDHIDRTKKKRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.227
R free: 0.2852
Average B factor: 86.357
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 283
Crystal growth procedure: 13% Tacsimate pH6.0
Matthews coefficient: 2.48
Solvent content (%): 50.4
Ligand: ADENOSINE (ADN)
Ligand formula: C10 H13 N5 O4
Ligand molecular weight: 267.241
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N
Ligand InChI: InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
Release date: 2024-03-27
Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues (PDB entry 5AQL)
Macromolecule: HEAT SHOCK COGNATE 71 KDA PROTEIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.51
Sequence length: 386 residues
Sequence: GPLGSMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLWSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1687
R free: 0.1965
Average B factor: 32.16
Crystallization pH: 8.5
Crystal growth procedure: 16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL
Matthews coefficient: 2.47
Solvent content (%): 50.19
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2016-10-05