satarupa22/MacromolecularLigandDB huggingface dataset:
Ternary complex of SUMO1 with the SIM of PML and zinc (PDB entry 8DJI)
Macromolecule: Small ubiquitin-related modifier 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 97 residues
Sequence: GSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYAQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.2308
R free: 0.2578
Average B factor: 34.7233
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM HEPES pH 7.0, 19 to 31 % (w/v) PEG 3350, and 1-5 mM zinc chloride
Matthews coefficient: 1.98
Solvent content (%): 38
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: 2022-08-10
hALK in complex with compound 7 N-((1S)-1-(5-fluoropyridin-2-yl)ethyl)-1-(5-methyl-1H-pyrazol-3-yl)-3-(oxetan-3-ylsulfonyl)-1H-pyrrolo[2,3-b]pyridin-6-amine (PDB entry 6E0R)
Macromolecule: ALK tyrosine kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 322 residues
Sequence: GAMGSTDYNPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.303
R work: 0.2375
R free: 0.296
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 16.75% PEG 3350, 2.% Tacsimate pH 7.0, 0.1M Tris Cl
Matthews coefficient: 2.11
Solvent content (%): 41.72
Ligand: N-[(1S)-1-(5-fluoropyridin-2-yl)ethyl]-1-(5-methyl-1H-pyrazol-3-yl)-3-[(oxetan-3-yl)sulfonyl]-1H-pyrrolo[2,3-b]pyridin-6-amine (HKJ)
Ligand formula: C21 H21 F N6 O3 S
Ligand molecular weight: 456.493
Ligand SMILES: Cc1cc(n[nH]1)n2cc(c3c2nc(cc3)NC(C)c4ccc(cn4)F)S(=O)(=O)C5COC5
Ligand InChI: InChI=1S/C21H21FN6O3S/c1-12-7-20(27-26-12)28-9-18(32(29,30)15-10-31-11-15)16-4-6-19(25-21(16)28)24-13(2)17-5-3-14(22)8-23-17/h3-9,13,15H,10-11H2,1-2H3,(H,24,25)(H,26,27)/t13-/m0/s1
Release date: 2019-05-01
Human jak1 kinase domain in complex with inhibitor (PDB entry 6GGH)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 292 residues
Sequence: TEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.18879
R free: 0.26186
Average B factor: 33.544
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 27% (m/v) PEG6000, 0.1 M MES/NaOH pH 6.0 and 5 mM DTT
Matthews coefficient: 2.52
Solvent content (%): 51.22
Ligand: ~{N}-[5-methyl-4-[7-[[(2~{R})-2-(4-methylpiperazin-1-yl)propanoyl]amino]-1~{H}-indol-3-yl]pyrimidin-2-yl]cyclopropanecarboxamide (EYQ)
Ligand formula: C25 H31 N7 O2
Ligand molecular weight: 461.559
Ligand SMILES: Cc1cnc(nc1c2c[nH]c3c2cccc3NC(=O)C(C)N4CCN(CC4)C)NC(=O)C5CC5
Ligand InChI: InChI=1S/C25H31N7O2/c1-15-13-27-25(30-24(34)17-7-8-17)29-21(15)19-14-26-22-18(19)5-4-6-20(22)28-23(33)16(2)32-11-9-31(3)10-12-32/h4-6,13-14,16-17,26H,7-12H2,1-3H3,(H,28,33)(H,27,29,30,34)/t16-/m1/s1
Release date: 2019-05-22
Post insertion complex of DNA polymerase Mu (K438A/Q441A) with 1-nt gapped DNA (PDB entry 7COD)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 482 residues
Sequence: MLPKRRRARVGSPSGDAASSTPPSTRFPGVAIYLVEPRMGRSRRAFLTGLARSKGFRVLDACSSEATHVVMEETSAEEAVSWQERRMAAAPPGCTPPALLDISWLTESLGAGQPVPVECRHRLEVAGPRKGPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSALFARELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1856
R free: 0.2109
Average B factor: 29.7598
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 1,4-Dioxane, Tris-Hcl, PEG 3350
Matthews coefficient: 1.95
Solvent content (%): 36.96
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: 2021-06-30
Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E121L-R123H mutant in complex with VSL12 at pH 6.0 (PDB entry 7A2Z)
Macromolecule: Tyrosine-protein kinase Fyn
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 60 residues
Sequence: GVTLFVALYDYEARTEDDLSFHKGEKFQIVNNTEGDWWLAHSLTTGETGYIPSNYVAPVD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.14
R work: 0.163
R free: 0.1948
Average B factor: 19.1827
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 1 M ammonium sulfate, 0.1 sodium acetate
Matthews coefficient: 2.09
Solvent content (%): 41.21
Release date: 2021-08-25
CRYSTAL STRUCTURE OF IRAK-4 WITH A 4,6-DIAMINONICOTINAMIDE INHIBITOR (COMPOUND NUMBER 9) (PDB entry 5W85)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 305 residues
Sequence: GAMGVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.227
R free: 0.251
Average B factor: 65.66
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Null
Matthews coefficient: 2.86
Solvent content (%): 57.02
Ligand: 6-[(1,3-benzothiazol-6-yl)amino]-4-{[(2S)-1-hydroxy-3-phenylpropan-2-yl]amino}-N-methylpyridine-3-carboxamide (9YS)
Ligand formula: C23 H23 N5 O2 S
Ligand molecular weight: 433.526
Ligand SMILES: CNC(=O)c1cnc(cc1NC(Cc2ccccc2)CO)Nc3ccc4c(c3)scn4
Ligand InChI: InChI=1S/C23H23N5O2S/c1-24-23(30)18-12-25-22(28-16-7-8-19-21(10-16)31-14-26-19)11-20(18)27-17(13-29)9-15-5-3-2-4-6-15/h2-8,10-12,14,17,29H,9,13H2,1H3,(H,24,30)(H2,25,27,28)/t17-/m0/s1
Release date: 2017-10-11
FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl [(7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-2-oxo-1,2,3,4,5,6,7,9-octahydro-11,8-(azeno)-1,9-benzodiazacyclotridecin-14-yl]carbamate (PDB entry 5Q0D)
Macromolecule: Coagulation factor XI
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.1718
R free: 0.192
Average B factor: 26.42
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM sodium acetate, pH 4.6, 25% (w/v) MePEG2000, 200 mM ammonium sulfate, then transferred to 100 mM Tris-HCl, pH 7.0, 25% (w/v) MePEG2000, 200 MM ammonium sulfate
Matthews coefficient: 3.44
Solvent content (%): 64.23
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: 2017-07-12
Crystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with isorhamnetin (PDB entry 6M8C)
Macromolecule: Inositol polyphosphate multikinase,Inositol polyphosphate multikinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.151
Sequence length: 261 residues
Sequence: GSFTSHQVAGHMYGKDKVGILQHPDGTVLKQLQPPPRGPRELEFYNMVYAADCFDGVLLELRKYLPKYYGIWSPPTAPNDLYLKLEDVTHKFNKPCIMDVKIGQKSYDPFASSEKIQQQVSKYPLMEEIGFLVLGMRVYHVHSDSYETENQHYGRSLTKETIKDGVSRFFHNGYCLRKDAVAASIQKIEKILQWFENQKQLNFYASSLLFVYEGSSQGGSGGEVEVRMIDFAHVFPSNTIDEGYVYGLKHLISVLRSILDN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.168
R free: 0.224
Average B factor: 23.87
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 10 mM isorhamnetin for 3 days.
Matthews coefficient: 2.21
Solvent content (%): 44.41
Ligand: isorhamnetin (IRH)
Ligand formula: C16 H12 O7
Ligand molecular weight: 316.262
Ligand SMILES: COc1cc(ccc1O)C2=C(C(=O)c3c(cc(cc3O2)O)O)O
Ligand InChI: InChI=1S/C16H12O7/c1-22-11-4-7(2-3-9(11)18)16-15(21)14(20)13-10(19)5-8(17)6-12(13)23-16/h2-6,17-19,21H,1H3
Release date: 2019-01-23
Structure of METTL3-METTL14(R298P) mutant methyltransferase complex (PDB entry 7RX7)
Macromolecule: N6-adenosine-methyltransferase 70 kDa subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.62
Sequence length: 225 residues
Sequence: MQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.645
R work: 0.1666
R free: 0.1877
Average B factor: 24.6641
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Tris (pH 8.0) and 20% PEG3350
Matthews coefficient: 2.32
Solvent content (%): 46.97
Release date: 2022-11-09
L. pneumophila effector kinase LegK7 (AMP-PNP bound) in complex with human MOB1A (PDB entry 6MCP)
Macromolecule: LegK7
Type: Protein, polypeptide(L)
Source organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
EC number: 2.7.11.1
Sequence length: 523 residues
Sequence: SNAKNTMPLVIAYNNAPEDDKIQKLFYLQKINYLLNKTQLNDDLFDWINDAEEGGWLNELAKFSINPNASFFLKGMQFAKAITEEIKNKPEINSSEVNIYHLMQERDQLLKEVEFEKCATRYAEINFLLNELALNDKKTKEIVERQTEILRLVAPKIKAIKGESIDNLPVIPSYKTKELGNHVNNFNFKFTMSGWEAPFVFRVEDRHELGKEQELHSYGVSKYFIEDYSVFMMRFKAEDGSTVYKPVILSQFANQNNLEEIAKQLKDGSPKNIAPRIGYYFVQLTDFCLKLIETHNYHPDIKLNNFLVHNNRVLVSDRKTFTTNDNPLASEILTSPLFAPDEFLKCLLFNKEGDPVGYNRNALWKRMNMPQFMAYQLGMALKQFLILTQLDELPDDFRNPDHSAVSHFKTPSRQIINLSLLVQELTRLDPDKRMTIKQFQTLLNFKNLPPDAFYQKVEEVFPSSQLGIAEDIEALNKVLNSDLKGEALLKQANPVFTKLSKYDPKETRLTRLAEKLAIRCFNN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1943
R free: 0.2333
Average B factor: 74.9598
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 288
Crystal growth procedure: 0.1 M HEPES, pH 7.5, 21% PEG600, 0.2 M sodium chloride, 20 mM succinate
Matthews coefficient: 2.78
Solvent content (%): 55.69
Ligand: TETRAETHYLENE GLYCOL (PG4)
Ligand formula: C8 H18 O5
Ligand molecular weight: 194.226
Ligand SMILES: C(COCCOCCOCCO)O
Ligand InChI: InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2
Release date: 2019-09-04
Semi-open conformation E3 ligase (PDB entry 6J1Y)
Macromolecule: NEDD4-like E3 ubiquitin-protein ligase WWP1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 519 residues
Sequence: GPGSEFQRPTMESVRNFEQWQSQRNQLQGAMQQFNQRYLYSASMLAAENDPYGPLPPGWEKRVDSTDRVYFVNHNTKTTQWEDPRTQGLQNEEPLPEGWEIRYTREGVRYFVDHNTRTTTFKDPRNGKSSVTKGGPQIAYERGFRWKLAHFRYLCQSNALPSHVKINVSRQTLFEDSFQQIMALKPYDLRRRLYVIFRGEEGLDYGGLAREWFFLLSHEVLNPMYCLFEYAGKNNYCLQINPASTINPDHLSYFCFIGRFIAMALFHGKFIDTGFSLPFYKRMLSKKLTIKDLESIDTEFYNSLIWIRDNNIEECGLEMYFSVDMEILGKVTSHDLKLGGSNILVTEENKDEYIGLMTEWRFSRGVQEQTKAFLDGFNEVVPLQWLQYFDEKELEVMLCGMQEVDLADWQRNTVYRHYTRNSKQIIWFWQFVKETDNEVRMRLLQFVTGTCRLPLGGFAELMGSNGPQKFCIEKVGKDTWLPRSHTCFNRLDLPPYKSYEQLKEKLLFAIEETEGFGQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.2081
R free: 0.2543
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289.15
Crystal growth procedure: 0.1M Sodium malonate pH 5.0, 12% w/v Polyethyleneglycol 3350
Matthews coefficient: 2.33
Solvent content (%): 47.12
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: 2019-07-24
Human Casein kinase 1 delta in complex with phosphorylated human PERIOD2 FASP peptide (PDB entry 8D7M)
Macromolecule: Casein kinase I isoform delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: GAMDPEFMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1807
R free: 0.2333
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.15 M Succinic Acid (5.5)
22% PEG 3350
Matthews coefficient: 2.49
Solvent content (%): 50.69
Release date: 2023-05-17
X-RAY STRUCTURE OF HDM2/CMR19 AT 1.45A: Discovery, X-ray structure and CPP-conjugation enabled uptake of p53/MDM2 macrocyclic peptide inhibitors (PDB entry 7NUS)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 96 residues
Sequence: GSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1766
R free: 0.1965
Average B factor: 12.38
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 2.2 M AmSO4, 0.2 M NaAcetate
Matthews coefficient: 2.36
Solvent content (%): 47.79
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: 2021-09-22
LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)((4,4-difluorocyclohexyl)methoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Compound N42) (PDB entry 6BGX)
Macromolecule: Lysine-specific demethylase 5A, linked KDM5A JMJ domain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.882
R work: 0.1986
R free: 0.2356
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.19
Solvent content (%): 43.74
Ligand: 2-{(S)-(2-chlorophenyl)[(4,4-difluorocyclohexyl)methoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (DKV)
Ligand formula: C22 H21 Cl F2 N2 O3
Ligand molecular weight: 434.864
Ligand SMILES: c1ccc(c(c1)C(c2cc3c([nH]2)c(ccn3)C(=O)O)OCC4CCC(CC4)(F)F)Cl
Ligand InChI: InChI=1S/C22H21ClF2N2O3/c23-16-4-2-1-3-14(16)20(30-12-13-5-8-22(24,25)9-6-13)18-11-17-19(27-18)15(21(28)29)7-10-26-17/h1-4,7,10-11,13,20,27H,5-6,8-9,12H2,(H,28,29)/t20-/m0/s1
Release date: 2018-03-28
Human PrimPol misinserting dATP opposite the 8-oxoguanine lesion (PDB entry 7JKP)
Macromolecule: DNA-directed primase/polymerase protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7
Sequence length: 354 residues
Sequence: MNRKWEAKLKQIEERASHYERKPLSSVYRPRLSKPEEPPSIWRLFHRQAQAFNFVKSCKEDVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKPANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFKDNIHVGNFLRKILQPALDLLGSEDDDSAPETTGHGFPHFSEAPARQGFSFNKMFTEKATEESWTSNSKKLERLGSAEQSSPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGKRVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEPSQNKQK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.592
R work: 0.2476
R free: 0.3066
Average B factor: 96.1665
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 225- 250 mM CaCl2 
16 -19% PEG 3350
Matthews coefficient: 2.36
Solvent content (%): 47.88
Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTP)
Ligand formula: C10 H16 N5 O12 P3
Ligand molecular weight: 491.182
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
Release date: 2021-06-30
Human JMJD5 in complex with MN and 5-((4-phenylbutyl)amino)pyridine-2,4-dicarboxylic acid. (PDB entry 7DYU)
Macromolecule: Bifunctional peptidase and arginyl-hydroxylase JMJD5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 235 residues
Sequence: STVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.1595
R free: 0.1946
Average B factor: 30.67
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride
Matthews coefficient: 2.36
Solvent content (%): 47.85
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: 2022-02-02
Structure of human galactokinase 1 bound with 4-{[2-(Methylsulfonyl)-1H-imidazol-1-yl]methyl}-1,3-thiazole (PDB entry 6QJE)
Macromolecule: Galactokinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.6
Sequence length: 392 residues
Sequence: HAALRQPQVAELLAEARRAFREEFGAEPELAVSAPGRVNLIGEHTDYNQGLVLPMALELMTVLVGSPRKDGLVSLLTTSEGADEPQRLQFPLPTAQRSLEPGTPRWANYVKGVIQYYPAAPLPGFSAVVVSSVPLGGGLSSSASLEVATYTFLQQLCPDSGTIAARAQVCQQAEHSFAGMPCGIMDQFISLMGQKGHALLIDCRSLETSLVPLSDPKLAVLITNSNVRHSLASSEYPVRRRQCEEVARALGAASLREVQLEELEAARDLVSKEGFRRARHVVGEIRRTAQAAAALRRGDYRAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMTGGGFGGCTVTLLEASAAPHAMRHIQEHYGGTATFYLSQAADGAKVLCL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.217
R free: 0.269
Average B factor: 60.7607
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MOPS/sodium HEPES pH 7.0-7.5, 40-50 % Morpheus Precipitant Mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1 M Morpheus Carboxylic acids mix (0.02M each of:sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate and sodium oxamate).
Matthews coefficient: 2.98
Solvent content (%): 58.77
Ligand: 2-(1,3-benzoxazol-2-ylamino)spiro[1,6,7,8-tetrahydroquinazoline-4,1'-cyclohexane]-5-one (HFK)
Ligand formula: C20 H22 N4 O2
Ligand molecular weight: 350.414
Ligand SMILES: c1ccc2c(c1)nc(o2)NC3=NC4(CCCCC4)C5=C(N3)CCCC5=O
Ligand InChI: InChI=1S/C20H22N4O2/c25-15-9-6-8-14-17(15)20(11-4-1-5-12-20)24-18(21-14)23-19-22-13-7-2-3-10-16(13)26-19/h2-3,7,10H,1,4-6,8-9,11-12H2,(H2,21,22,23,24)
Release date: 2019-02-27
Crystal structure of CDK9-Cyclin T1 bound by compound 6 (PDB entry 7NWK)
Macromolecule: Cyclin-dependent kinase 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 330 residues
Sequence: MAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFPITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNSQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDFFWSDPMPSDLKGMLST
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.81
R work: 0.18
R free: 0.205
Average B factor: 66.17
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 14% PEG1000, 100 mM sodium potassium phosphate, pH 6.2, 500 mM NaCl, 4 mM TCEP
Matthews coefficient: 4.16
Solvent content (%): 70.42
Ligand: N-((1R,3R)-3-(7-(4-fluoro-2-methoxyphenyl)-3H-imidazo[4,5-b]pyridin-2-yl)cyclopentyl)acetamide (UT5)
Ligand formula: C20 H21 F N4 O2
Ligand molecular weight: 368.405
Ligand SMILES: CC(=O)NC1CCC(C1)c2[nH]c3c(ccnc3n2)c4ccc(cc4OC)F
Ligand InChI: InChI=1S/C20H21FN4O2/c1-11(26)23-14-5-3-12(9-14)19-24-18-16(7-8-22-20(18)25-19)15-6-4-13(21)10-17(15)27-2/h4,6-8,10,12,14H,3,5,9H2,1-2H3,(H,23,26)(H,22,24,25)/t12-,14-/m1/s1
Release date: 2021-10-27
DNA Polymerase Lambda, dCTP:At Mn2+ Product State Ternary Complex, 420 min (PDB entry 7M4I)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 329 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.005
R work: 0.2218
R free: 0.247
Average B factor: 59.4261
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.85
Solvent content (%): 56.79
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: 2022-07-06