satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of the FK1 domain of the FKBP51 G64S variant in complex with (1S,5S,6R)-10-((3,5-dichlorophenyl)sulfonyl)-5-(hydroxymethyl)-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one (PDB entry 8BAJ)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNSKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1751
R free: 0.2096
Average B factor: 13.269
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 40% PEG3350 0.1M HEPES-NaOH pH 7.5 0.2M ammonium acetate
Matthews coefficient: 2.24
Solvent content (%): 45.21
Ligand: (1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-5-(hydroxymethyl)-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one (9QN)
Ligand formula: C21 H23 Cl2 N3 O4 S
Ligand molecular weight: 484.396
Ligand SMILES: c1ccnc(c1)CN2CC(C3CCCC(C2=O)N3S(=O)(=O)c4cc(cc(c4)Cl)Cl)CO
Ligand InChI: InChI=1S/C21H23Cl2N3O4S/c22-15-8-16(23)10-18(9-15)31(29,30)26-19-5-3-6-20(26)21(28)25(11-14(19)13-27)12-17-4-1-2-7-24-17/h1-2,4,7-10,14,19-20,27H,3,5-6,11-13H2/t14-,19-,20+/m1/s1
Release date: 2022-11-16
An open conformation Form 1 of switch II for RhoA (PDB entry 7WZA)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: YFQGMAAIRKKLVIVGDGAVGKTSLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMVFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMETSAKTKDGVREVFEMATRAALQA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.50028778245
R work: 0.187176443169
R free: 0.219733346012
Average B factor: 19.0578590928
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 20% PEG 3350, 0.2M potassium formate
Matthews coefficient: 2.12
Solvent content (%): 41.92
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: 2023-02-22
Crystal structure of death-associated protein kinase 1 in complex with resveratrol and MES (PDB entry 7CCW)
Macromolecule: Death-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 293 residues
Sequence: MTVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.17
R free: 0.1875
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.8 M ammonium sulfate, 0.1 M MES-NaOH pH 6.5, 14.4 mg/mL DAPK1, 2 mM resveratrol
Matthews coefficient: 2.03
Solvent content (%): 35.39
Ligand: RESVERATROL (STL)
Ligand formula: C14 H12 O3
Ligand molecular weight: 228.243
Ligand SMILES: c1cc(ccc1C=Cc2cc(cc(c2)O)O)O
Ligand InChI: InChI=1S/C14H12O3/c15-12-5-3-10(4-6-12)1-2-11-7-13(16)9-14(17)8-11/h1-9,15-17H/b2-1+
Release date: 2021-01-20
Crystal structure of the human fat mass and obesity associated protein (FTO) in complex with CCO10 (PDB entry 4QHO)
Macromolecule: Alpha-ketoglutarate-dependent dioxygenase FTO
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 495 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMTPKDDEFYQQWQLKYPKLILREASSVSEELHKEVQEAFLTLHKHGCLFRDLVRIQGKDLLTPVSRILIGNPGCTYKYLNTRLFTVPWPVKGSNIKHTEAEIAAACETFLKLNDYLQIETIQALEELAAKEKANEDAVPLCMSADFPRVGMGSSYNGQDEVDIKSRAAYNVTLLNFMDPQKMPYLKEEPYFGMGKMAVSWHHDENLVDRSAVAVYSYSCEGPEEESEDDSHLEGRDPDIWHVGFKISWDIETPGLAIPLHQGDCYFMLDDLNATHQHCVLAGSQPRFSSTHRVAECSTGTLDYILQRCQLALQNVCDDVDNDDVSLKSFEPAVLKQGEEIHNEVEFEWLRQFWFQGNRYRKCTDWWCQPMAQLEALWKKMEGVTNAVLHEVKREGLPVEQRNEILTAILASLTARQNLRREWHARCQSRIARTLPADQKPECRPYWEKDDASMPLPFDLTDIVSELRGQLLEAKP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.37
R work: 0.1769
R free: 0.2076
Average B factor: 86.97
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 100mM trisodium citrate, 8% PEG 3350, 4% tert-butanol, 8mg/ml protein, 1mM ZnSO4, 1mM inhibitor, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 2.84
Solvent content (%): 56.72
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: 2015-06-03
crystal structure of Human Methionine aminopeptidase (HsMetAP1b) in complex with AN-P2-5H-06 (PDB entry 6LZB)
Macromolecule: Methionine aminopeptidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 329 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMLEDPYRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKLLSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCYPSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHGDLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHAQANGFSVVRSYCGHGIHKLFHTAPNVPHYAKNKAVGVMKSGHVFTIEPMICEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSARPHFMS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.1626
R free: 0.1998
Average B factor: 25.322
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.2
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M Bistris pH-6.2, 19% PEG 3350, 5% Glycerol
Matthews coefficient: 2.42
Solvent content (%): 49.13
Ligand: COBALT (II) ION (CO)
Ligand formula: Co
Ligand molecular weight: 58.933
Ligand SMILES: [Co+2]
Ligand InChI: InChI=1S/Co/q+2
Release date: 2021-02-24
Crystal Structure of human phosphodiesterase 10 in complex with N-(3-methyl-1-pyridin-2-ylthieno[2,3-c]pyrazol-5-yl)benzamide (PDB entry 5SIN)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.193
R free: 0.2623
Average B factor: 47.346
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.65
Solvent content (%): 53.55
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: 2022-10-12
Crystal Structure of Human Indoleamine 2,3-dioxygenagse 1 (hIDO1) Complexed with (1R,2S)-2-(((5-bromo-1H-indazol-4-yl)amino)methyl)Cyclohexan-1-ol (36) (PDB entry 7E0T)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 392 residues
Sequence: SKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.137
R work: 0.2129
R free: 0.2723
Average B factor: 64.2554
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 15% to 23% PEG 8000, 0.2M ammonium acetate
Matthews coefficient: 3.11
Solvent content (%): 60.46
Ligand: (1~{R},2~{S})-2-[[(5-bromanyl-1~{H}-indazol-4-yl)amino]methyl]cyclohexan-1-ol (HU9)
Ligand formula: C14 H18 Br N3 O
Ligand molecular weight: 324.216
Ligand SMILES: c1cc(c(c2c1[nH]nc2)NCC3CCCCC3O)Br
Ligand InChI: InChI=1S/C14H18BrN3O/c15-11-5-6-12-10(8-17-18-12)14(11)16-7-9-3-1-2-4-13(9)19/h5-6,8-9,13,16,19H,1-4,7H2,(H,17,18)/t9-,13+/m0/s1
Release date: 2021-07-21
Crystal Structure of SETD2 Bound to an Indole-based Inhibitor (PDB entry 7TY3)
Macromolecule: Histone-lysine N-methyltransferase SETD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.359
Sequence length: 278 residues
Sequence: GETSVPPGSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKKNKSHRDIKRMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGKMKKERSRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2136
R free: 0.2695
Average B factor: 64.88
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Potassium thiocyanate, 0.1 M Tris pH 7.5, 18% w/v PEG 2000 MME
Matthews coefficient: 2.36
Solvent content (%): 47.86
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: 2022-08-31
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMOPL000475a (PDB entry 5QI3)
Macromolecule: Poly [ADP-ribose] polymerase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 183 residues
Sequence: SMFYGTVSSPDSGVYEMKIGSIIFQVASGDITKEEADVIVNSTSNSFNLKAGVSKAILECAGQNVERECSQQAQQRKNDYIITGGGFLRCKNIIHVIGGNDVKSSVSSVLQECEKKNYSSICLPAIGTGNAKQHPDKVAEAIIDAIEDFVQKGSAQSVKKVKVVIFLPQVLDVFYANMKKREG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.05
R work: 0.1399
R free: 0.1576
Average B factor: 12.445
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 80 mM KBr, 30 % PEG2kMME
Matthews coefficient: 2
Solvent content (%): 38.64
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2019-04-10
The structure of D77G hCINAP-ADP (PDB entry 5JZV)
Macromolecule: Adenylate kinase isoenzyme 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.4.3
Sequence length: 206 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMLLPNILLTGTPGVGKTTLGKELASKSGLKYINVGDLAREEQLYDGYDEEYDCPILDEDRVVDELDNQMREGGVIVGYHGCDFFPERWFHIVFVLRTDTNVLYERLETRGYNEKKLTDNIQCEIFQVLYEEATASYKEEIVHQLPSNKPEELENNVDQILKWIEQWIKDHNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.19
R free: 0.235
Average B factor: 34.76
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.01M MAGNESIUM CHLORIDE HEXAHYDRATE,
 0.05M MES MONOHYDRATE PH 5.6, 1.8M LITHIUM SULFATE MONOHYDRATE,
 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Matthews coefficient: 3.73
Solvent content (%): 67.03
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2016-08-10
Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with N-PNT-DNM 15 (PDB entry 8CB1)
Macromolecule: Lysosomal alpha-glucosidase (76 kDa)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.20
Sequence length: 123 residues
Sequence: QCDVPPNSRFDCAPDKAITQEQCEARGCCYIPAKQGLQGAQMGQPWCFFPPSYPSYKLENLSSSEMGYTATLTRTTPTFFPKDILTLRLDVMMETENRLHFTIKDPANRRYEVPLETPRVHSR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.14224
R free: 0.1749
Average B factor: 40.587
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 1.9 M AMMONIUM SULPHATE, 0.1 M HEPES, 2% V/V PEG400
Matthews coefficient: 3.4
Solvent content (%): 62.79
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2023-09-13
Y271G DNA polymerase beta substrate complex with a templating cytosine and incoming rGTP (PDB entry 6UOL)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACCGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.936
R work: 0.1865
R free: 0.2496
Average B factor: 25.205
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 19% PEG3350, 0.35 M sodium acetate, 0.05 M Imidazole, pH 8.0.
Matthews coefficient: 2.32
Solvent content (%): 46.97
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2020-01-08
Crystal structure of C-terminal Domain of MSK1 in complex with covalently bound pyrrolopyrimidine compound 27 (co-crystal) (PDB entry 7UP8)
Macromolecule: Ribosomal protein S6 kinase alpha-5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 306 residues
Sequence: GMKDSPFYQHYDLDLKDKPLGEGSFSICRKCVHKKSNQAFAVKIISKRMEANTQKEITALKLCEGHPNIVKLHEVFHDQLHTFLVMELLNGGELFERIKKKKHFSETEASYIMRKLVSAVSHMHDVGVVHRDLKPENLLFTDENDNLEIKIIDFGFARLKPGSGNGYDESCDLWSLGVILYTMLSGQVPFQSHDRSLTCTSAVEIMKKIKKGDFSFEGEAWKNVSQEAKDLIQGLLTVDPNKRLKMSGLRYNEWLQDGSQLSSNPLMTPDILGSSGAAVHTCVKATFHAFNKYKREGFCLQNVDKA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.1863
R free: 0.2625
Average B factor: 57.99
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 289
Crystal growth procedure: Plate 320267f8, puck cnl-6-9.Screen:Morpheus_D8_F8_G8_Index_E7. To prepare the ligand complex, PID7059-1 was exchanged to 25 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol, 1 mM BME (dillution buffer) using a GE (GE28-9180-04) spin column. The protein was diluted to 1 mg/ml in dilution bufffer and 150 ?M UCB1710266 in 100% DMSO_D6 was added. The complex was incubated at 4 C for an hour, then excess ligand was removed by dialysis using a D-tube dialyzer in 250 ml dilution buffer, overnight at 4 ?C. The following day the protein was concentrated to 10.1 mg/ml and setup 200:100 ul protein:well solution. Crystals were flash frozen in 100% well solution
Matthews coefficient: 2.31
Solvent content (%): 46.72
Ligand: (5M)-5-(5-bromo-2-chloropyrimidin-4-yl)-5H-pyrrolo[3,2-d]pyrimidine (O10)
Ligand formula: C10 H5 Br Cl N5
Ligand molecular weight: 310.537
Ligand SMILES: c1cn(c2c1ncnc2)c3c(cnc(n3)Cl)Br
Ligand InChI: InChI=1S/C10H5BrClN5/c11-6-3-14-10(12)16-9(6)17-2-1-7-8(17)4-13-5-15-7/h1-5H
Release date: 2022-07-06
Crystal structure of the unliganded tandem bromodomain (BD1, BD2) of human TAF1 (PDB entry 7JJH)
Macromolecule: Transcription initiation factor TFIID subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 265 residues
Sequence: SMSIHRRRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELESLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1875
R free: 0.2198
Average B factor: 46.8533
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.8 M Succinic Acid, pH 7.0
Matthews coefficient: 4.24
Solvent content (%): 71
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2021-01-27
GTPase HRAS mutant D33K under ambient pressure (PDB entry 7OGD)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 166 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYKPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.181
R free: 0.25
Average B factor: 27.67
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: 1.96
Solvent content (%): 37.11
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: 2022-02-09
THE JAK3 KINASE DOMAIN IN COMPLEX WITH A COVALENT INHIBITOR (PDB entry 5WFJ)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 293 residues
Sequence: GPASQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGSERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.48
R work: 0.2
R free: 0.255
Average B factor: 52.96
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Matthews coefficient: 2.4
Solvent content (%): 48.67
Ligand: 4-({[3-(propanoylamino)phenyl]methyl}amino)pyrrolo[1,2-b]pyridazine-3-carboxamide (9Z4)
Ligand formula: C18 H19 N5 O2
Ligand molecular weight: 337.376
Ligand SMILES: CCC(=O)Nc1cccc(c1)CNc2c3cccn3ncc2C(=O)N
Ligand InChI: InChI=1S/C18H19N5O2/c1-2-16(24)22-13-6-3-5-12(9-13)10-20-17-14(18(19)25)11-21-23-8-4-7-15(17)23/h3-9,11,20H,2,10H2,1H3,(H2,19,25)(H,22,24)
Release date: 2017-10-04
Bruton's tyrosine kinase in complex with an orthosteric inhibitor (PDB entry 8FLH)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 283 residues
Sequence: GPLGSKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1956
R free: 0.2285
Average B factor: 21.43
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: bis-tris, ammonium salt, PEG
Matthews coefficient: 2.3
Solvent content (%): 46.51
Ligand: 2-(3,5-dichloroanilino)-1-{(3R)-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]azepan-1-yl}ethan-1-one (Y8H)
Ligand formula: C21 H24 Cl2 N6 O
Ligand molecular weight: 447.361
Ligand SMILES: CN(c1c2cc[nH]c2ncn1)C3CCCCN(C3)C(=O)CNc4cc(cc(c4)Cl)Cl
Ligand InChI: InChI=1S/C21H24Cl2N6O/c1-28(21-18-5-6-24-20(18)26-13-27-21)17-4-2-3-7-29(12-17)19(30)11-25-16-9-14(22)8-15(23)10-16/h5-6,8-10,13,17,25H,2-4,7,11-12H2,1H3,(H,24,26,27)/t17-/m1/s1
Release date: 2023-03-01
Structure of TTBK1 kinase domain in complex with Compound 3 (PDB entry 7JXX)
Macromolecule: Tau-tubulin kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 332 residues
Sequence: GHMSGGGEQADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKAGTDALLSTSTSTPPQQNTRQTAAMFGVVNV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1797
R free: 0.2126
Average B factor: 34.64
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1M TRIS pH 8.5, 0.2M Na Acetate 20% PEG3350
Matthews coefficient: 1.86
Solvent content (%): 34.01
Ligand: 4-(2-amino-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2-b]indol-11-yl)-2-methylbut-3-yn-2-ol (VP7)
Ligand formula: C20 H20 N4 O
Ligand molecular weight: 332.399
Ligand SMILES: CC(C)(C#Cc1ccc2c(c1)c-3c([nH]2)CCCc4c3nc(nc4)N)O
Ligand InChI: InChI=1S/C20H20N4O/c1-20(2,25)9-8-12-6-7-15-14(10-12)17-16(23-15)5-3-4-13-11-22-19(21)24-18(13)17/h6-7,10-11,23,25H,3-5H2,1-2H3,(H2,21,22,24)
Release date: 2021-05-19
X-ray structure of furin in complex with the guanylhydrazone-based inhibitor 4 (mi359) (PDB entry 7O22)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 480 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.169
R free: 0.1825
Average B factor: 33.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: CRYSTALLIZATION SOLUTION: 100mM MES, 200mM K/NAH2PO4, PH 5.5, 2 M NACL; RESERVOIR SOLUTION: 3.0-3.2M NACL
Matthews coefficient: 3.69
Solvent content (%): 66.7
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: 2021-09-01