satarupa22/MacromolecularLigandDB huggingface dataset:
Identification of novel, potent and selective GCN2 inhibitors as first-in-class anti-tumor agents (PDB entry 6N3O)
Macromolecule: eIF-2-alpha kinase GCN2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 317 residues
Sequence: GGSSETQRQFSRYFIEFEELQLLGKGAFGAVIKVQNKLDGCCYAVKRIPINPASRQFRRIKGEVTLLSRLHHENIVRYYNAWIENGCHESEPSVTTEAVHYLYIQMEYCEASTLRDTIDQGLYRDTVRLWRLFREILDGLAYIHEKGMIHRNLKPVNIFLDSDDHVKIGDFGLATDHLAFSADSKQDDQTGDLIKSDPSGHLEGMVGEALYVSPEVQGSTKSAYNQKVDLFSLGIIFFEMSYHPMVTASERIFVLNQLRDPTSPKFPEDFDDGEHAKQKSVISWLLNHDPAKRPTATELLKSELLPPPQMEESELHE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1992
R free: 0.2544
Average B factor: 84.3
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Na Citrate pH 5.6, 8% PEG 6K, 0.7 M LiCl, 1% Ethylene Glycol
Matthews coefficient: 2.65
Solvent content (%): 53.64
Ligand: N-{3-[(2-aminopyrimidin-5-yl)ethynyl]-2,4-difluorophenyl}-5-chloro-2-methoxypyridine-3-sulfonamide (KA7)
Ligand formula: C18 H12 Cl F2 N5 O3 S
Ligand molecular weight: 451.834
Ligand SMILES: COc1c(cc(cn1)Cl)S(=O)(=O)Nc2ccc(c(c2F)C#Cc3cnc(nc3)N)F
Ligand InChI: InChI=1S/C18H12ClF2N5O3S/c1-29-17-15(6-11(19)9-23-17)30(27,28)26-14-5-4-13(20)12(16(14)21)3-2-10-7-24-18(22)25-8-10/h4-9,26H,1H3,(H2,22,24,25)
Release date: 2019-10-09
Crystal structure of fragment 3-(1,3-Benzothiazol-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain (PDB entry 6CEF)
Macromolecule: Histone deacetylase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 107 residues
Sequence: GSPLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNKFGEDMPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1501
R free: 0.1809
Average B factor: 12.606
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 291
Crystal growth procedure: 2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol
Matthews coefficient: 2.09
Solvent content (%): 41.07
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: 2018-02-28
Crystal structure of human ATAD2 bromodomain in complex with N-(4-bromo-3-(3-methylpyrrolidin-1-yl)sulfonyl)phenyl)-2-(-4-cyclopropyl-4-methyl-2,5-dioxoimidazolidin-1-yl)acetamide (PDB entry 6YB4)
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): 1.85
R work: 0.1902
R free: 0.2152
Average B factor: 30.81
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M trisHCl pH 7.0-8.0, 1.2-1.5M ammonium sulphate
Matthews coefficient: 4.06
Solvent content (%): 69.73
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: 2020-05-06
Crystal Structure of 2-Hydroxycyclohepta-2,4,6-triene-1-thione bound to human carbonic anhydrase 2 (PDB entry 5THN)
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): 1.33
R work: 0.17575
R free: 0.20602
Average B factor: 12.35
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium Sulfate, Tris, pH 8.0 VAPOR DIFFUSION, temperature 291K
Matthews coefficient: 2.05
Solvent content (%): 39.9
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: 2017-04-26
Cdc7-Dbf4 bound to ADP-BeF3 (PDB entry 6YA8)
Macromolecule: Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 359 residues
Sequence: MLAGVKKDIEKLYEAVPQLSNVFKIEDKIGEGTFSSVYLATAQLQVGPEEKIALKHLIPTSHPIRIAAELQCLTVAGGQDNVMGVKYCFRKNDHVVIAMPYLEHESFLDILNSLSFQEVREYMLNLFKALKRIHQFGIVHRDVKPSNFLYNRRLKKYALVDFGLAQGTHDTKIELLKFVQSEAQQERCSQNKPASLTCDCYATDKVCSICLSRRQQVAPRAGTPGFRAPEVLTKCPNQTTAIDMWSAGVIFLSLLSGRYPFYKASDDLTALAQIMTIRGSRETIQAAKTFGKSILCSKEVPAQDLRKLCERLRGAGAGGWNEVPDEAYDLLDKLLDLNPASRITAEEALLHPFFKDMSL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1656
R free: 0.197
Average B factor: 26.29
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.57
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1M MMT pH 6.57, 21% PEG 1500, 15% v/v Acetonitrile, 20mM MgCl2
Matthews coefficient: 2.17
Solvent content (%): 43.2
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: 2020-05-27
Crystal structure of B30.2 PRYSPRY domain of MID2 (PDB entry 7QRZ)
Macromolecule: Probable E3 ubiquitin-protein ligase MID2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 190 residues
Sequence: SMNSQPFKLDPKMTHKKLKISNDGLQMEKDESSLKKSHTPERFSGTGCYGAAGNIFIDSGCHYWEVVMGSSTWYAIGIAYKSAPKNEWIGKNASSWVFSRCNSNFVVRHNNKEMLVDVPPHLKRLGVLLDYDNNMLSFYDPANSLHLHTFDVTFILPVCPTFTIWNKSLMILSGLPAPDFIDYPERQECN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1624
R free: 0.1921
Average B factor: 24.777
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 18% High molecular weight PEG smears, 0.1M ADA pH 6.5, 0.2M ammonium sulfate
Matthews coefficient: 2.17
Solvent content (%): 43.37
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: 2022-05-04
Bovine GRK2 in complex with Gbetagamma subunits and CCG215022 (PDB entry 5HE0)
Macromolecule: Beta-adrenergic receptor kinase 1
Type: Protein, polypeptide(L)
Source organism: Bos taurus
EC number: 2.7.11.15
Sequence length: 641 residues
Sequence: KKILLPEPSIRSVMQKYLEDRGEVTFEKIFSQKLGYLLFRDFCLKHLEEAKPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIMKELLACSHPFSKSAIEHVQGHLVKKQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFCQWKNVELNIHLTMNDFSVHRIIGRGGFGEVYGCRKADTGKMYAMKCLDKKRIKMKQGETLALNERIMLSLVSTGDCPFIVCMSYAFHTPDKLSFILDLMNGGDLHYHLSQHGVFSEADMRFYAAEIILGLEHMHNRFVVYRDLKPANILLDEHGHVRISDLGLACDFSKKKPHASVGTHGYMAPEVLQKGVAYDSSADWFSLGCMLFKLLRGHSPFRQHKTKDKHEIDRMTLTMAVELPDSFSPELRSLLEGLLQRDVNRRLGCLGRGAQEVKESPFFRSLDWQMVFLQKYPPPLIPPRGEVNAADAFDIGSFDEEDTKGIKLLDSDQELYRNFPLTISERWQQEVAETVFDTINAETDRLEARKKTKNKQLGHEEDYALGKDCIMHGYMSKMGNPFLTQWQRRYFYLFPNRLEWRGEGEAPQSLLTMEEIQSVEETQIKERKCLLLKIRGGKQFVLQCDSDPELVQWKKELRDAYREAQQLVQRVPKMKNKPRA
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.56
R work: 0.2017
R free: 0.264
Average B factor: 71.102
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 50 mM MES, 0.8-1.2 M sodium chloride, 8-16% PEG3350
Matthews coefficient: 3.47
Solvent content (%): 64.51
Ligand: (4S)-4-{4-fluoro-3-[(pyridin-2-ylmethyl)carbamoyl]phenyl}-N-(1H-indazol-5-yl)-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxamide (453)
Ligand formula: C26 H22 F N7 O3
Ligand molecular weight: 499.496
Ligand SMILES: CC1=C(C(NC(=O)N1)c2ccc(c(c2)C(=O)NCc3ccccn3)F)C(=O)Nc4ccc5c(c4)cn[nH]5
Ligand InChI: InChI=1S/C26H22FN7O3/c1-14-22(25(36)32-17-6-8-21-16(10-17)12-30-34-21)23(33-26(37)31-14)15-5-7-20(27)19(11-15)24(35)29-13-18-4-2-3-9-28-18/h2-12,23H,13H2,1H3,(H,29,35)(H,30,34)(H,32,36)(H2,31,33,37)/t23-/m0/s1
Release date: 2016-05-11
Covalent Inhibitor 4a bound to the Lipid Pocket of p38alpha Mutant S251C (PDB entry 5O8V)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKICSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.20598
R free: 0.26906
Average B factor: 43.332
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM MES pH 5.6-6.2
20-30 % PEG4000
Matthews coefficient: 2.28
Solvent content (%): 46.03
Ligand: ~{N}-[3-[7-azanyl-4-(2-phenylethylamino)quinazolin-2-yl]phenyl]propanamide (9O2)
Ligand formula: C25 H25 N5 O
Ligand molecular weight: 411.499
Ligand SMILES: CCC(=O)Nc1cccc(c1)c2nc3cc(ccc3c(n2)NCCc4ccccc4)N
Ligand InChI: InChI=1S/C25H25N5O/c1-2-23(31)28-20-10-6-9-18(15-20)24-29-22-16-19(26)11-12-21(22)25(30-24)27-14-13-17-7-4-3-5-8-17/h3-12,15-16H,2,13-14,26H2,1H3,(H,28,31)(H,27,29,30)
Release date: 2017-09-06
Crystal structure of a Ube2S-ubiquitin conjugate (PDB entry 5BNB)
Macromolecule: Ubiquitin-conjugating enzyme E2 S
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2.19
Sequence length: 156 residues
Sequence: MNSNVENLPPHIIRLVYKEVTTLTADPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKDFPASPPKGYFLTKIFHPNVGANGEICVNVLKRDWTAELGIRHVLLTIKMLLIHPNPESALNEEAGRLLLENYEEYAARARLLTEIHG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.49
R work: 0.243
R free: 0.304
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris, 20% PEG 4000
Matthews coefficient: 2.31
Solvent content (%): 46.76
Release date: 2016-02-17
Crystal structure of human Cathepsin-S with bound ligand (PDB entry 5QC5)
Macromolecule: Cathepsin S
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.27
Sequence length: 223 residues
Sequence: ILPDSVDWREKGCVTEVKYQGSCGASWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEILQGGG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.18
R free: 0.256
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Matthews coefficient: 2.15
Solvent content (%): 42.87
Ligand: 1-[5-{1-[3-(4-tert-butylpiperidin-1-yl)propyl]-5-(methylsulfonyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-3-yl}-2-(trifluoromethyl)phenyl]-N-[(4-fluorophenyl)methyl]methanamine (BAJ)
Ligand formula: C34 H45 F4 N5 O2 S
Ligand molecular weight: 663.812
Ligand SMILES: CC(C)(C)C1CCN(CC1)CCCn2c3c(c(n2)c4ccc(c(c4)CNCc5ccc(cc5)F)C(F)(F)F)CN(CC3)S(=O)(=O)C
Ligand InChI: InChI=1S/C34H45F4N5O2S/c1-33(2,3)27-12-17-41(18-13-27)15-5-16-43-31-14-19-42(46(4,44)45)23-29(31)32(40-43)25-8-11-30(34(36,37)38)26(20-25)22-39-21-24-6-9-28(35)10-7-24/h6-11,20,27,39H,5,12-19,21-23H2,1-4H3
Release date: 2017-12-20
Structure of human Usb1 with uridine-uridine, inactive H208Q mutant (PDB entry 6D30)
Macromolecule: U6 snRNA phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 191 residues
Sequence: GAHMGNWATHVYVPYEAKEEFLDLLDVLLPHAQTYVPRLVRMKVFHLSLSQSVVLRHHWILPFVQALKARMTSFHRFFFTANQVKIYTNQEKTRTFIGLEVTSGHAQFLDLVSEVDRVMEEFNLTTFYQDPSFQLSLAWCVGDARLQLEGQCLQELQAIVDGFEDAEVLLRVHTEQVRCKSGNKFFSMPLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.17
R work: 0.1494
R free: 0.1717
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Tris, 25% SOKALN CP 42, 10% tetrahydrofuran
Matthews coefficient: 2.07
Solvent content (%): 40.45
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: 2018-09-05
Structure of a hypothetical protease (PDB entry 6J8O)
Macromolecule: Small vasohibin-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 49 residues
Sequence: GSPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTEL
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.855
R work: 0.177
R free: 0.1945
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M BIS-TRIS pH 6.5, 16% polyethylene glycol 10000
Matthews coefficient: 2.87
Solvent content (%): 57.11
Release date: 2020-01-22
X-ray structure of the human PP1 gamma catalytic subunit treated with hydrogen peroxide (PDB entry 4UT3)
Macromolecule: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 323 residues
Sequence: MADLDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAEKKKPNATRPVTPPRGMITKQAKK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.19
R work: 0.17336
R free: 0.21146
Average B factor: 47.211
Crystallization pH: 9
Crystal growth procedure: 7-12% PEG3350, 0.1 M BICINE, PH 9.0 SOAKING IN RESERVOIR ENRICHED WITH 50MM H2O2 FOR 10 MINS CRYOPROTECTION IN RESEVOIR ENRICHED WITH 25% MPD
Matthews coefficient: 2.46
Solvent content (%): 49.96
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: 2015-07-22
Crystal Structure Matriptase (C731S) in Complex with Inhibitor MM1132-2 (PDB entry 8G1V)
Macromolecule: Suppressor of tumorigenicity 14 protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.109
Sequence length: 241 residues
Sequence: VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGFRYSDPTQWTAFLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIALLELEKPAEYSSMVRPISLPDASHVFPAGKAIWVTGWGHTQYGGTGALILQKGEIRVINQTTCENLLPQQITPRMMCVGFLSGGVDSCQGDSGGPLSSVEADGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTGV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.1309
R free: 0.152
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 2M ammonium sulfate, 100 sodium cacodylate, 200 mM NaCl
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: 2024-07-10
The structure of Artemis variant D37A (PDB entry 7AFS)
Macromolecule: Protein artemis
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 362 residues
Sequence: SMSSFEGQMAEYPTISIDRFDRENLRARAYFLSHCHKAHMKGLRAPTLKRRLECSLKVYLYCSPVTKELLLTSPKYRFWKKRIISIEIETPTQISLVDEASGEKEEIVVTLLPAGHCPGSVMFLFQGNNGTVLYTGDFRLAQGEAARMELLHSGGRVKDIQSVYLDTTFCDPRFYQIPSREECLSGVLELVRSWITRSPYHVVWLNCKAAYGYEYLFTNLSEELGVQVHVNKLDMFRNMPEILHHLTTDRNTQIHACRHPKAEEYFQWSKLPCGITSRNRIPLHIISIKPSTMWFGERSRKTNVIVRTGESSYRACFSFHSSYSEIKDFLSYLCPVNAYPNVIPVGTTMDKVVEILKPLCRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1859
R free: 0.2161
Average B factor: 25.925
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.2 M Ammonium Acetate, 0.1 M Bis-TRIS pH 5.5, 25% PEG 3350
Matthews coefficient: 1.92
Solvent content (%): 36.09
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2020-10-28
Falcilysin in complex with hemoglobin alpha chain peptide (PDB entry 8WXW)
Macromolecule: Falcilysin
Type: Protein, polypeptide(L)
Source organism: Plasmodium falciparum 3D7
EC number: 3.4.24
Sequence length: 1158 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMEWIHEKSPKHNSYDIIEKRYNEEFKMTYTVYQHKKAKTQVISLGTNDPLDVEQAFAFYVKTLTHSGKGIPHILQHSVLSGSKNYNYKNSIGLLEKGTLHTHLNAYTFNDRTVYMAGSMNNKDFFNIMGVYMDSVFQPNVLENKYIFETEGWTYEVEKLKEDEKGKAEIPQMKDYKVSFNGIVYNEMKGALSSPLEDLYHEEMKYMFPDNVHSNNSGGDPKEITNLTYEEFKEFYYKNYNPKKVKVFFFSKNNPTELLNFVDQYLGQLDYSKYRDDAVESVEYQTYKKGPFYIKKKYGDHSEEKENLVSVAWLLNPKVDKTNNHNNNHSNNQSSENNGYSNGSHSSDLSLENPTDYFVLLIINNLLIHTPESVLYKALTDCGLGNNVIDRGLNDSLVQYIFSIGLKGIKRNNEKIKNFDKVHYEVEDVIMNALKKVVKEGFNKSAVEASINNIEFILKEANLKTSKSIDFVFEMTSKLNYNRDPLLIFEFEKYLNIVKNKIKNEPMYLEKFVEKHFINNAHRSVILLEGDENYAQEQENLEKQELKKRIENFNEQEKEQVIKNFEELSKYKNAEESPEHLNKFPIISISDLNKKTLEVPVNVYFTNINENNNIMETYNKLKTNEHMLKDNMDVFLKKYVLKNDKHNTNNNNNNNNNMDYSFTETKYEGNVPILVYEMPTTGIVYLQFVFSLDHLTVDELAYLNLFKTLILENKTNKRSSEDFVILREKNIGSMSANVALYSKDDHLNVTDKYNAQALFNLEMHVLSHKCNDALNIALEAVKESDFSNKKKVIDILKRKINGMKTTFSEKGYAILMKYVKAHLNSKHYAHNIIYGYENYLKLQEQLELAENDFKTLENILVRIRNKIFNKKNLMVSVTSDYGALKHLFVNSNESLKNLVSYFEENDKYINDMQNKVNDPTVMGWNEEIKSKKLFDEEKVKKEFFVLPTFVNSVSMSGILFKPGEYLDPSFTVIVAALKNSYLWDTVRGLNGAYGVFADIEYDGSVVFLSARDPNLEKTLATFRESAKGLRKMADTMTENDLLRYIINTIGTIDKPRRGIELSKLSFLRLISNESEQDRVEFRKRIMNTKKEDFYKFADLLESKVNEFEKNIVIITTKEKANEYIANVDGEFKKVLIE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1889
R free: 0.2096
Average B factor: 37.72
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 4% w/v PEG 1500, 20% v/v glycerol
Matthews coefficient: 2.28
Solvent content (%): 46.07
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: 2024-08-07
Crystal Structure of Thrombin in complex with compound40 (PDB entry 6ZUW)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1658
R free: 0.2135
Average B factor: 35.252
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 283
Crystal growth procedure: 0.02 M phosphate buffer pH 7.5, 
27% PEG 8000, 100 mM NaCl
Matthews coefficient: 2.51
Solvent content (%): 51.06
Ligand: [2-[[(1~{R})-1-(3-chlorophenyl)ethyl]amino]-7-methoxy-1,3-benzoxazol-5-yl]-[(2~{S},5~{R})-5-ethyl-2-(2-hydroxyethyl)-2-methyl-morpholin-4-yl]methanone (QQK)
Ligand formula: C26 H32 Cl N3 O5
Ligand molecular weight: 502.002
Ligand SMILES: CCC1COC(CN1C(=O)c2cc3c(c(c2)OC)oc(n3)NC(C)c4cccc(c4)Cl)(C)CCO
Ligand InChI: InChI=1S/C26H32ClN3O5/c1-5-20-14-34-26(3,9-10-31)15-30(20)24(32)18-12-21-23(22(13-18)33-4)35-25(29-21)28-16(2)17-7-6-8-19(27)11-17/h6-8,11-13,16,20,31H,5,9-10,14-15H2,1-4H3,(H,28,29)/t16-,20-,26+/m1/s1
Release date: 2020-08-26
Carbonic Anhydrase 2 in Complex with Steriod_Sulphamoyl AKI_13 (PDB entry 8OLK)
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): 1.27
R work: 0.13594
R free: 0.16888
Average B factor: 16.484
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-H2SO4
Matthews coefficient: 2.08
Solvent content (%): 40.85
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2024-04-10
Human neurofibromin 2/merlin residues 1-339 in complex with LATS1 (PDB entry 7LWH)
Macromolecule: Merlin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 339 residues
Sequence: MAGAIASRMSFSSLKRKQPKTFTVRIVTMDAEMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFLAKFYPENAEEELVQEITQHLFFLQVKKQILDEKIYCPPEASVLLASYAVQAKYGDYDPSVHKRGFLAQEELLPKRVINLYQMTPEMWEERITVWYAEHRGRARDEAEMEYLKIAQDLEMYGVNYFAIRNKKGTELLLGVDALGLHIYDPENRLTPKISFPWNEIRNISYSDKEFTIKPLDKKIDVFKFNSSKLRVNKLILQLCIENHDLFMRRRKADSLEVQQMKAQAREEKARKQMERQRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.606
R work: 0.205
R free: 0.2325
Average B factor: 33.45
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 600 mM imidazole (pH 6.5), 15% (w/v) polyethylene glycol 3,350
Matthews coefficient: 2.67
Solvent content (%): 53.86
Ligand: IMIDAZOLE (IMD)
Ligand formula: C3 H5 N2
Ligand molecular weight: 69.085
Ligand SMILES: c1c[nH+]c[nH]1
Ligand InChI: InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)/p+1
Release date: 2021-08-11
Crystal structure of Sirt2 in complex with selective inhibitor L55 (PDB entry 5YQN)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 306 residues
Sequence: GASGSERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1735
R free: 0.2038
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M HEPES PH7.4, 30% PEG 3350
Matthews coefficient: 2.12
Solvent content (%): 41.92
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: 2018-10-17