satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of Human Inositol Polyphosphate Multikinase (IPMK) Catalytic Core Domain (PDB entry 6E7F)
Macromolecule: Inositol polyphosphate multikinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.151
Sequence length: 278 residues
Sequence: MHHHHHHENLYFQGMDGTVLKQLQPPPRGPRELEFYNMVYAADCFDGVLLELRKYLPKYYGIWSPPTAPNDLYLKLEDVTHKFNKPCIMDVKIGQKSYDPFASSEKIQQQVSKYPLMEEIGFLVLGMRVYHVHSDSYETENQHYGRSLTKETIKDGVSRFFHNGYCLRKDAVAASIQKIEKILQWFENQKQLNFYASSLLFVYEGSSQPTTTKLNDRTLAEKFLSGGGGSGGGGSQEIAEVEVRMIDFAHVFPSNTIDEGYVYGLKHLISVLRSILDN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2265
R free: 0.2803
Average B factor: 57
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M sodium citrate, pH 3.5, 0.8 M (NH4)2 SO4, 1 mM AMPPNP, 1 mM MnCl2, 0.73 mM Inositol (1,3,4,6)tetra phosphate (IP4)
Matthews coefficient: 3.05
Solvent content (%): 65.17
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2018-11-07
Crystal structure of the human CHIP-TPR domain in complex with a 10mer acetylated tau peptide (PDB entry 8FYU)
Macromolecule: E3 ubiquitin-protein ligase CHIP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 128 residues
Sequence: KSPSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQHEQALADCRRALELDGQSVKAHFFLGQCQLEMESYDEAIANLQRAYSLAKEQRLNFGDDIPSALRIAKKKRWNS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84839139202
R work: 0.203977935651
R free: 0.243637622496
Average B factor: 25.9315874363
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M CaCl2, 0.1 M HEPES (pH 7.4). 28% PEG 4K
Matthews coefficient: 1.85
Solvent content (%): 33.64
Release date: 2023-08-30
Human N-acylethanolamine-hydrolyzing acid amidase (NAAA) precursor (C126A) (PDB entry 6DXW)
Macromolecule: N-acylethanolamine-hydrolyzing acid amidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.60
Sequence length: 341 residues
Sequence: DRHHHHHHKLSPPAAPRFNVSLDSVPELRWLPVLRHYDLDLVRAAMAQVIGDRVPKWVHVLIGKVVLELERFLPQPFTGEIRGMCDFMNLSLADALLVNLAYESSVFATSIVAQDSRGHIYHGRNLDYPFGNVLRKLTVDVQFLKNGQIAFTGTTFIGYVGLWTGQSPHKFTVSGDERDKGWWWENAIAALFRRHIPVSWLIRATLSESENFEAAVGKLAKTPLIADVYYIVGGTSPREGVVITRNRDGPADIWPLDPLNGAWFRVETNYDHWKPAPKEDDRRTSAIKALNATGQANLSLEALFQILSVVPVYNNFTIYTTVMSAGSPDKYMTRIRNPSRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1673
R free: 0.1933
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 1 M LiCl, 0.1 M MES pH 6 and 10 % PEG 6000
Matthews coefficient: 3.25
Solvent content (%): 62.18
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2018-09-26
Crystal structure of the SET domain of the human MLL5 methyltransferase (PDB entry 5HT6)
Macromolecule: Histone-lysine N-methyltransferase 2E
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 138 residues
Sequence: GPTNNLLFKPPVESHIQKNKKILKSAKDLPPDALIIEYRGKFMLREQFEANGYFFKRPYPFVLFYSKFHGLEMCVDARTFGNEARFIRRSCTPNAEVRHEIQDGTIHLYIYSIHSIPKGTEITIAFDFDYGNAKYKVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.093
R work: 0.2089
R free: 0.2424
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M NH4Cl, 12 % (w/v) PEG 3350
Matthews coefficient: 2.2
Solvent content (%): 44.01
Release date: 2016-11-16
Crystal structure of the catalytic domain of human JARID1B in complex with pyruvate (PDB entry 5FY9)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.1991
R free: 0.2342
Crystallization pH: 7.5
Crystal growth procedure: 0.1M HEPES PH 7.5, 0.8M POTASSIUM PHOSPHATE DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC
Matthews coefficient: 2.11
Solvent content (%): 41.64
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2017-03-22
SYK Kinase domain in complex with azabenzimidazole inhibitor 7 (PDB entry 6ZCR)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 299 residues
Sequence: MDTEVYESPYADPEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.188
R free: 0.218
Average B factor: 34.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 0.1M Na3Cit pH 6.4, 16% PEG3350, 0.2M KH2PO4
Matthews coefficient: 2.06
Solvent content (%): 40.22
Ligand: 6-chloro-2-(2-fluoro-4,5-dimethoxyphenyl)-N-(piperidin-4-ylmethyl)-3H-imidazo[4,5-b]pyridin-7-amine (5JG)
Ligand formula: C20 H23 Cl F N5 O2
Ligand molecular weight: 419.88
Ligand SMILES: COc1cc(c(cc1OC)F)c2[nH]c3c(n2)c(c(cn3)Cl)NCC4CCNCC4
Ligand InChI: InChI=1S/C20H23ClFN5O2/c1-28-15-7-12(14(22)8-16(15)29-2)19-26-18-17(13(21)10-25-20(18)27-19)24-9-11-3-5-23-6-4-11/h7-8,10-11,23H,3-6,9H2,1-2H3,(H2,24,25,26,27)
Release date: 2021-06-23
Crystal Structure of human phosphodiesterase 10 in complex with 2-chloro-6-ethyl-N-(2-phenyl-[1,2,4]triazolo[1,5-a]pyridin-7-yl)pyridine-4-carboxamide (PDB entry 5SEZ)
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): 1.99
R work: 0.1758
R free: 0.2176
Average B factor: 36.516
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: 2.64
Solvent content (%): 53.49
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
Discovery of Functionally Selective Transforming Growth Factor beta Type II Receptor (TGF-beta RII) Inhibitors as Anti-Fibrosis Agents (PDB entry 7DV6)
Macromolecule: TGF-beta receptor type-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 323 residues
Sequence: MAHNTELLPIELDTLVGKGRFAEVYKAKLKQNTSEQFETVAVKIFPYEEYASWKTEKDIFSDINLKHENILQFLTAEERKTELGKQYWLITAFHAKGNLQEYLTRHVISWEDLRKLGSSLARGIAHLHSDHTPCGRPKMPIVHRDLKSSNILVKNDLTCCLCDFGLSLRLDPTLSVDDLANSGQVGTARYMAPEVLASAMNLENVESFKQTDVYSMALVLWEMTSRCNAVGEVKDYEPPFGSKVREHPCVASMADNVLADAGRPEIPSFWLNHQGIQMVCETLTECWDHDPEARLTAQCVAERFSELEHLDRLSGLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.39
R work: 0.15967
R free: 0.22391
Average B factor: 46.599
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 12-22% PEG4000,3% Ethylene Glycol,16% glycerol, 160 mM MgCl2, 80 mM TrisHCl at pH 7.5-9.3,The 9.2 mg/mL of TGFbetaRII protein was incubated with 1mM compound at 277K for 1-2 hr
Matthews coefficient: 2.5
Solvent content (%): 50.73
Ligand: 5-[(3S)-5,5-dimethyloxolan-3-yl]-6-methoxy-3-(2-methoxypyridin-4-yl)pyrazolo[1,5-a]pyrimidine (HJF)
Ligand formula: C19 H22 N4 O3
Ligand molecular weight: 354.403
Ligand SMILES: CC1(CC(CO1)c2c(cn3c(n2)c(cn3)c4ccnc(c4)OC)OC)C
Ligand InChI: InChI=1S/C19H22N4O3/c1-19(2)8-13(11-26-19)17-15(24-3)10-23-18(22-17)14(9-21-23)12-5-6-20-16(7-12)25-4/h5-7,9-10,13H,8,11H2,1-4H3/t13-/m1/s1
Release date: 2021-06-16
Complex structure of human protein kinase CK2 catalytic subunit with a thieno[2,3-d]pyrimidin inhibitor crystallized under high-salt conditions (PDB entry 5M44)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 335 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.71
R work: 0.2186
R free: 0.2593
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: Protein stock solution: 6 mg/ml CK2alpha1-335 in 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5;
Inhibitor stock solution: 10 mM inhibitor in DMSO;
Protein/inhibitor complex solution: 90 microliter protein stock solution + 10 microliter inhibitor stock solution;
Reservoir solution: 4.2 M NaCl, 0.1 M sodium citrate, pH 5.0;
Drop solution before equlibration: 0.5 microliter  protein/inhibitor complex solution + 0.5 microliter reservoir solution
Matthews coefficient: 2.13
Solvent content (%): 42.3
Ligand: 3-[5-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]sulfanylpropanoic acid (7EY)
Ligand formula: C16 H14 N2 O2 S2
Ligand molecular weight: 330.425
Ligand SMILES: Cc1ccc(cc1)c2csc3c2c(ncn3)SCCC(=O)O
Ligand InChI: InChI=1S/C16H14N2O2S2/c1-10-2-4-11(5-3-10)12-8-22-16-14(12)15(17-9-18-16)21-7-6-13(19)20/h2-5,8-9H,6-7H2,1H3,(H,19,20)
Release date: 2017-01-18
System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: NEDD4L and UbV NL.1 (PDB entry 5HPK)
Macromolecule: E3 ubiquitin-protein ligase NEDD4-like
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 383 residues
Sequence: GSREFKQKYDYFRKKLKKPADIPNRFEMKLHRNNIFEESYRRIMSVKRPDVLKARLWIEFESEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFTFIGRVAGLAVFHGKLLDGFFIRPFYKMMLGKQITLNDMESVDSEYYNSLKWILENDPTELDLMFCIDEENFGQTYQVDLKPNGSEIMVTNENKREYIDLVIQWRFVNRVQKQMNAFLEGFTELLPIDLIKIFDENELELLMCGLGDVDVNDWRQHSIYKNGYCPNHPVIQWFWKAVLLMDAEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQLFTIEQWGSPEKLPRAHTCFNRLDLPPYETFEDLREKLLMAVENAQGFEGVD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.431
R work: 0.2114
R free: 0.2268
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: Sodium cacodylate, NaCl, PEG 8000, 1-butanol
Matthews coefficient: 4.45
Solvent content (%): 72.35
Release date: 2016-03-16
RT XFEL structure of CypA solved using MESH injection system (PDB entry 6U5C)
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): 1.62
R work: 0.1362
R free: 0.1569
Average B factor: 26.29
Crystallization method: BATCH MODE
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM HEPES, pH 7.5, 5 mM TCEP, 20% PEG3350
Matthews coefficient: 2.8
Solvent content (%): 56.09
Release date: 2020-01-29
Crystal structure of CHK1 complex with compound 9 (PDB entry 7BKO)
Macromolecule: Serine/threonine-protein kinase Chk1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICINKMLNHENVVKFYGHRREGNIQYLFLEYCSGGELFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPENLLLDERDNLKISDFGLATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRPRVTSGGVSESPSGHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2415
R free: 0.3307
Average B factor: 51.648
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 10-30% PEG8K
0.1M HEPES pH 7.5
15% isopropanol
Matthews coefficient: 2.51
Solvent content (%): 51.01
Ligand: 1H-pyrazolo[3,4-d]pyrimidin-4-amine (TVW)
Ligand formula: C5 H5 N5
Ligand molecular weight: 135.127
Ligand SMILES: c1c2c(ncnc2n[nH]1)N
Ligand InChI: InChI=1S/C5H5N5/c6-4-3-1-9-10-5(3)8-2-7-4/h1-2H,(H3,6,7,8,9,10)
Release date: 2021-07-07
Near full length Kidney type Glutaminase in complex with 2,2-Dimethyl-2,3-Dihydrobenzo[a] Phenanthridin-4(1H)-one (DDP) (PDB entry 8GWR)
Macromolecule: Glutaminase kidney isoform, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.2
Sequence length: 669 residues
Sequence: MMRLRGSGMLRDLLLRSPAGVSATLRRAQPLVTLCRRPRGGGRPAAGPAAAARLHPWWGGGGWPAEPLARGLSSSPSEILQELGKGSTHPQPGVSPPAAPAAPGPKDGPGETDAFGNSEGKELVASGENKIKQGLLPSLEDLLFYTIAEGQEKIPVHKFITALKSTGLRTSDPRLKECMDMLRLTLQTTSDGVMLDKDLFKKCVQSNIVLLTQAFRRKFVIPDFMSFTSHIDELYESAKKQSGGKVADYIPQLAKFSPDLWGVSVCTVDGQRHSTGDTKVPFCLQSCVKPLKYAIAVNDLGTEYVHRYVGKEPSGLRFNKLFLNEDDKPHNPMVNAGAIVVTSLIKQGVNNAEKFDYVMQFLNKMAGNEYVGFSNATFQSERESGDRNFAIGYYLKEKKCFPEGTDMVGILDFYFQLCSIEVTCESASVMAATLANGGFCPITGERVLSPEAVRNTLSLMHSCGMYDFSGQFAFHVGLPAKSGVAGGILLVVPNVMGMMCWSPPLDKMGNSVKGIHFCHDLVSLCNFHNYDNLRHFAKKLDPRREGGDQRVKSVINLLFAAYTGDVSALRRFALSAMDMEQRDYDSRTALHVAAAEGHVEVVKFLLEACKVNPFPKDRWNNTPMDEALHFGHHDVFKILQEYQVQYTPQGDSDNGKENQTVHKNLDGLL
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.801
R work: 0.2042
R free: 0.2362
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5M sodium malonate pH 7, 4% jeffamine
Matthews coefficient: 3.37
Solvent content (%): 63.5
Ligand: 2,2-dimethyl-1,3-dihydrobenzo[a]phenanthridin-4-one (HZO)
Ligand formula: C19 H17 N O
Ligand molecular weight: 275.344
Ligand SMILES: CC1(Cc2c(cnc3c2c4ccccc4cc3)C(=O)C1)C
Ligand InChI: InChI=1S/C19H17NO/c1-19(2)9-14-15(17(21)10-19)11-20-16-8-7-12-5-3-4-6-13(12)18(14)16/h3-8,11H,9-10H2,1-2H3
Release date: 2022-12-21
Human Carbonic Anhydrase II in complex with 4-Methylbenzenesulfonamide (PDB entry 6GM9)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 265 residues
Sequence: GSPEFMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.089
R work: 0.1032
R free: 0.1184
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: Ammoniumsulfate 2.70 M, pH = 7.8, saturated with p-Chloromercurybenzoic acid
Matthews coefficient: 2.06
Solvent content (%): 40.44
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: 2019-06-19
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 4-diphosphoinositol pentakisphosphate (4-IP7), Mg, and Fluoride ion (PDB entry 6WOB)
Macromolecule: Diphosphoinositol polyphosphate phosphohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.52
Sequence length: 169 residues
Sequence: HHHHHHSSGVDLGTENLYFQSMMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1602
R free: 0.2028
Average B factor: 17.64
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 10% (w/v) PEG 8000, 10% (v/v) isopropanol, 200 mM Li2SO4, 75 mM NaAc, pH 5.5 and 25 mM HEPES, pH 7.0 and soaking in solution of 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 20 mM MgCl2 and 80 mM NaF in present of 2mM 4-IP7
Matthews coefficient: 2.12
Solvent content (%): 42.05
Ligand: (1S,2R,3S,4S,5S,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate (U71)
Ligand formula: C6 H19 O27 P7
Ligand molecular weight: 740.015
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C6H19O27P7/c7-34(8,9)27-1-2(28-35(10,11)12)4(30-37(16,17)18)6(32-40(25,26)33-39(22,23)24)5(31-38(19,20)21)3(1)29-36(13,14)15/h1-6H,(H,25,26)(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3-,4+,5-,6-/m0/s1
Release date: 2021-03-03
2.2 Angstrom Crystal Structure of a Human Arginyl-tRNA Synthetase (PDB entry 4ZAJ)
Macromolecule: Arginine--tRNA ligase, cytoplasmic
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.19
Sequence length: 601 residues
Sequence: MINIISRLQEVFGHAIKAAYPDLENPPLLVTPSQQAKFGDYQCNSAMGISQMLKTKEQKVNPREIAENITKHLPDNECIEKVEIAGPGFINVHLRKDFVSEQLTSLLVNGVQLPALGENKKVIVDFSSPNIAKEMHVGHLRSTIIGESISRLFEFAGYDVLRLNHVGDWGTQFGMLIAHLQDKFPDYLTVSPPIGDLQVFYKESKKRFDTEEEFKKRAYQCVVLLQGKNPDITKAWKLICDVSRQELNKIYDALDVSLIERGESFYQDRMNDIVKEFEDRGFVQVDDGRKIVFVPGCSIPLTIVKSDGGYTYDTSDLAAIKQRLFEEKADMIIYVVDNGQSVHFQTIFAAAQMIGWYDPKVTRVFHAGFGVVLGEDKKKFKTRSGETVRLMDLLGEGLKRSMDKLKEKERDKVLTAEELNAAQTSVAYGCIKYADLSHNRLNDYIFSFDKMLDDRGNTAAYLLYAFTRIRSIARLANIDEEMLQKAARETKILLDHEKEWKLGRCILRFPEILQKILDDLFLHTLCDYIYELATAFTEFYDSCYCVEKDRQTGKILKVNMWRMLLCEAVAAVMAKGFDILGIKPVQRMENLYFQSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.2189
R free: 0.2643
Average B factor: 33.206
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 1000
Matthews coefficient: 2.63
Solvent content (%): 53.17
Release date: 2016-03-30
DCN1 covalently bound to inhibitor 4 (PDB entry 6XOQ)
Macromolecule: Lysozyme, DCN1-like protein 1 chimera
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 386 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNAMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWAEAAVNLAKSRWYNQTPNRTKRVITTFATGTWDAYKNLRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.202
R free: 0.247
Average B factor: 31.02
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 28-33% PEG 3350, 0.2 M ammonium formate
Matthews coefficient: 2.1
Solvent content (%): 41.41
Ligand: (2E)-N-[(2S)-2-cyclohexyl-2-({N-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alanyl}amino)ethyl]-4-(morpholin-4-yl)but-2-enamide (H9S)
Ligand formula: C32 H47 N5 O4 S
Ligand molecular weight: 597.812
Ligand SMILES: CCC(=O)NC(Cc1nc2ccc(cc2s1)C(C)C)C(=O)NC(CNC(=O)C=CCN3CCOCC3)C4CCCCC4
Ligand InChI: InChI=1S/C32H47N5O4S/c1-4-29(38)34-26(20-31-35-25-13-12-24(22(2)3)19-28(25)42-31)32(40)36-27(23-9-6-5-7-10-23)21-33-30(39)11-8-14-37-15-17-41-18-16-37/h8,11-13,19,22-23,26-27H,4-7,9-10,14-18,20-21H2,1-3H3,(H,33,39)(H,34,38)(H,36,40)/b11-8+/t26-,27+/m0/s1
Release date: 2021-06-02
Crystal structure of the Bro domain of HD-PTP (PDB entry 5CRU)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 23
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 361 residues
Sequence: MEAVPRMPMIWLDLKEAGDFHFQPAVKKFVLKNYGENPEAYNEELKKLELLRQNAVRVPRDFEGCSVLRKYLGQLHYLQSRVPMGSGQEAAVPVTWTEIFSGKSVAHEDIKYEQACILYNLGALHSMLGAMDKRVSEEGMKVSCTHFQCAAGAFAYLREHFPQAYSVDMSRQILTLNVNLMLGQAQECLLEKSMLDNRKSFLVARISAQVVDYYKEACRALENPDTASLLGRIQKDWKKLVQMKIYYFAAVAHLHMGKQAEEQQKFGERVAYFQSALDKLNEAIKLAKGQPDTVQDALRFTMDVIGGKYNSAKKDNDFIYHEAVPALDTLQPVKGAPLVKPLPVNPTDPAVTGPDIFAKLV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.22
R free: 0.2594
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 293
Crystal growth procedure: 0.03 M HEPES sodium, 16%(w/v) polyethylene glycol 3350, 0.67%(w/v) tryptone, 0.03 M urea
Matthews coefficient: 2.21
Solvent content (%): 44.26
Release date: 2016-02-24
CBP bromodomain complexed with YF2-23 (PDB entry 7JUO)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 118 residues
Sequence: GSKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2104
R free: 0.2758
Average B factor: 58.076
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M lithium citrate tribasic tetrahydrate, 17-19% PEG 3350, pH 8.4
Matthews coefficient: 2.55
Solvent content (%): 51.77
Ligand: N-{1-[1,1-di(pyridin-2-yl)ethyl]-6-(1-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-3-yl)-1H-indol-4-yl}ethanesulfonamide (YF2)
Ligand formula: C30 H28 N6 O3 S
Ligand molecular weight: 552.647
Ligand SMILES: CCS(=O)(=O)Nc1cc(cc2c1ccn2C(C)(c3ccccn3)c4ccccn4)c5cn(c6c5C=CNC6=O)C
Ligand InChI: InChI=1S/C30H28N6O3S/c1-4-40(38,39)34-24-17-20(23-19-35(3)28-21(23)11-15-33-29(28)37)18-25-22(24)12-16-36(25)30(2,26-9-5-7-13-31-26)27-10-6-8-14-32-27/h5-19,34H,4H2,1-3H3,(H,33,37)
Release date: 2021-09-01