satarupa22/MacromolecularLigandDB huggingface dataset:
JAK2-JH2 (PDB entry 7F7W)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 275 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCFCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAWAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.2068
R free: 0.2383
Average B factor: 42.41
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.1M Tris, pH 8.0 0.2M Sodium acetate, 12-20% PEG 4000
Matthews coefficient: 2.27
Solvent content (%): 45.72
Ligand: 2-((1-(2-fluoro-4-((4-(1-isopropyl-1H-pyrazol-4-yl)-5-methylpyrimidin-2-yl)amino)phenyl)piperidin-4-yl)(methyl)amino)ethan-1-ol (36H)
Ligand formula: C25 H34 F N7 O
Ligand molecular weight: 467.582
Ligand SMILES: Cc1cnc(nc1c2cnn(c2)C(C)C)Nc3ccc(c(c3)F)N4CCC(CC4)N(C)CCO
Ligand InChI: InChI=1S/C25H34FN7O/c1-17(2)33-16-19(15-28-33)24-18(3)14-27-25(30-24)29-20-5-6-23(22(26)13-20)32-9-7-21(8-10-32)31(4)11-12-34/h5-6,13-17,21,34H,7-12H2,1-4H3,(H,27,29,30)
Release date: 2022-03-30
Structure of DDB1 bound to DS17-engaged CDK12-cyclin K (PDB entry 8BU1)
Macromolecule: DNA damage-binding protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 840 residues
Sequence: GGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.98
R work: 0.1934
R free: 0.2181
Average B factor: 104.35
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive
Matthews coefficient: 3.93
Solvent content (%): 68.68
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2023-09-13
Binary Complex of Human DNA Polymerase Mu with MgdGTP (PDB entry 6IPN)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.20772
R free: 0.2361
Average B factor: 16.745
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M HEPES pH 7.5, 1.5 M Li2SO4
Matthews coefficient: 2.46
Solvent content (%): 49.92
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: 2019-05-29
Post-catalytic nicked complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and newly incorporated dCMP (PDB entry 6P1Q)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 354 residues
Sequence: GSAAASPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1689
R free: 0.2064
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 100mM HEPES pH 7.5, 100mM NaCl, 10% w/v PEG4000
Matthews coefficient: 2.82
Solvent content (%): 57
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: 2019-09-04
Structure of CO2 bound apo-form of human carbonic anhydrase II with 0 sec (no) warming (PDB entry 5DSO)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.11209
R free: 0.15907
Average B factor: 15.859
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.3M sodium citrate, 100mM TrisHCl pH 7.8
Matthews coefficient: 2.06
Solvent content (%): 40.19
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: 2016-05-04
The Crystal Structure of human PARP14 from Biortus. (PDB entry 7D2C)
Macromolecule: Protein mono-ADP-ribosyltransferase PARP14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2
Sequence length: 197 residues
Sequence: MGSSHHHHHHENLYFQGFYGTVSSPDSGVYEMKIGSIIFQVASGDITKEEADVIVNSTSNSFNLKAGVSKAILECAGQNVERECSQQAQQRKNDYIITGGGFLRCKNIIHVIGGNDVKSSVSSVLQECEKKNYSSICLPAIGTGNAKQHPDKVAEAIIDAIEDFVQKGSAQSVKKVKVVIFLPQVLDVFYANMKKRE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1752
R free: 0.1969
Average B factor: 12.332
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M NaCl, 0.1M Tris pH8.5, 25% PEG3350
Matthews coefficient: 1.77
Solvent content (%): 30.56
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: 2020-09-30
EED in complex with PRC2 allosteric inhibitor EED709 (PDB entry 5H15)
Macromolecule: Polycomb protein EED
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 367 residues
Sequence: GKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.27
R work: 0.1826
R free: 0.2357
Average B factor: 26.84
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris, 16% PEG 8000, 10 mM beta-Nicotinamide mononucleotide
Matthews coefficient: 2.3
Solvent content (%): 46.57
Ligand: (3R,4S)-1-[(2-methoxyphenyl)methyl]-N,N-dimethyl-4-(1-methylindol-3-yl)pyrrolidin-3-amine (LQD)
Ligand formula: C23 H29 N3 O
Ligand molecular weight: 363.496
Ligand SMILES: Cn1cc(c2c1cccc2)C3CN(CC3N(C)C)Cc4ccccc4OC
Ligand InChI: InChI=1S/C23H29N3O/c1-24(2)22-16-26(13-17-9-5-8-12-23(17)27-4)15-20(22)19-14-25(3)21-11-7-6-10-18(19)21/h5-12,14,20,22H,13,15-16H2,1-4H3/t20-,22+/m1/s1
Release date: 2017-01-25
Crystal structure of human carbonic anhydrase isozyme I with 4-[(2-Hydroxyethyl)thio]benzenesulfonamide (PDB entry 4WUP)
Macromolecule: Carbonic anhydrase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSPDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.185
R free: 0.232
Average B factor: 24.864
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M TrisHCl (pH 8.5), 
0.2M ammonium acetate and 24% of PEG4000
Matthews coefficient: 2.37
Solvent content (%): 47.6
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: 2015-07-01
Crystal Structure of the Human mitochondrial Cysteine Desulfurase in complex with ISD11 and E. coli ACP1 protein at 2.75A (PDB entry 5WGB)
Macromolecule: Cysteine desulfurase, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.8.1.7
Sequence length: 426 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMLEMLRPLYMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVASLIGADPREIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGFQVTYLPVQKSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHTDAAQAVGKIPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGMRSGTVPTPLVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYPGCINLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIGRFTTEEEVDYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2127
R free: 0.2553
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 285
Crystal growth procedure: 0.1 M MES pH 6.5
0.3 M Ammonium Acetate
20 mM Calcium Acetate
20 mM CaCl2
19 % isopropanol
Matthews coefficient: 2.9
Solvent content (%): 57.65
Ligand: PYRIDOXAL-5'-PHOSPHATE (PLP)
Ligand formula: C8 H10 N O6 P
Ligand molecular weight: 247.142
Ligand SMILES: Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
Ligand InChI: InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
Release date: 2017-07-26
Human Sirt6 in complex with ADP-ribose and fragment 3-aminobenzamide (PDB entry 8AKF)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.1839
R free: 0.225
Average B factor: 43.132
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Matthews coefficient: 2.59
Solvent content (%): 52.6
Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL
[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE (AR6)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
Release date: 2023-08-16
Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B (PDB entry 7UJP)
Macromolecule: Calcium/calmodulin-dependent protein kinase type II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 268 residues
Sequence: TRFTEEYQLFEELGKGAFSVVRRCVKVLAGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGHHYLIFDLVTGGELFEDIVAREYYSEADASHCIQQILEAVLHCHQMGVVHRNLKPENLLLASKLKGAAVKLADFGLAIEVEGEQQAWFGFAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYKQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPSKRITAAEALKHPWISHR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.56
R work: 0.2318
R free: 0.2808
Average B factor: 29.88
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.2
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane, 0.1 M Ammonium sulfate, 25% PEG 3350, 19mM Methyl 6-O-(N-heptylcarbamoyl)-alpha-D-glucopyranoside
Matthews coefficient: 2.31
Solvent content (%): 46.69
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: 2022-04-13
HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 9 AT 1.13A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes (PDB entry 6Q9L)
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: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.13
R work: 0.1782
R free: 0.1898
Average B factor: 11.377
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 2.7M AmSO4, 0.2M NaI, 0.2M NaCl, 0.2M TRIS
Matthews coefficient: 2.07
Solvent content (%): 40.44
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: 2019-05-15
Structure of protein kinase ck2 catalytic subunit (csnk2a1 gene product) in complex with the bivalent inhibitor KN2 (PDB entry 7AT5)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 349 residues
Sequence: MGSSHHHHHHSQDPMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.1739
R free: 0.1947
Average B factor: 40.29
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: reservoir composition: 30 % (w/v) PEG8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5; crystallization drop composition before equilibration: 0.01 ml reservoir solution plus 0.02 ml enzyme stock solution (6 mg/ml enzyme, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5); the bivalent inhibitor KN2 was introduced by extensive soaking
Matthews coefficient: 3.19
Solvent content (%): 61.49
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: 2021-08-04
Methyltransferase domain of human suppressor of variegation 3-9 homolog 2 (SUV39H2) in complex with OTS186935 inhibitor (PDB entry 6P0R)
Macromolecule: Histone-lysine N-methyltransferase SUV39H2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 299 residues
Sequence: PKDNNKTLKPAIAEYIVKKAKQRIALQRWQDELNRRKNHKGMIFVENTVDLEGPPSDFYYINEYKPAPGISLVNEATFGCSCTDCFFQKCCPAEAGVLLAYNKNQQIKIPPGTPIYECNSRCQCGPDCPNRIVQKGTQYSLCIFRTSNGRGWGVKTLVKIKRMSFVMEYVGEVITSEEAERRGQFYDNKGITYLFDLDYESDEFTVDAARYGNVSHFVNHSCDPNLQVFNVFIDNLDTRLPRIALFSTRTINAGEELTFDYQMKGSGDISSDSIDHSPAKKRVRTVCKCGAVTCRGYLN
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2123
R free: 0.2667
Average B factor: 42.46
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG3350, 0.2M NH4Formate
Matthews coefficient: 2.07
Solvent content (%): 40.49
Ligand: (3S)-1-[2-(5-chloro-2,4-dimethoxyphenyl)imidazo[1,2-a]pyridin-7-yl]-N-[(pyridin-4-yl)methyl]pyrrolidin-3-amine (NM4)
Ligand formula: C25 H26 Cl N5 O2
Ligand molecular weight: 463.959
Ligand SMILES: COc1cc(c(cc1c2cn3ccc(cc3n2)N4CCC(C4)NCc5ccncc5)Cl)OC
Ligand InChI: InChI=1S/C25H26ClN5O2/c1-32-23-13-24(33-2)21(26)12-20(23)22-16-31-10-6-19(11-25(31)29-22)30-9-5-18(15-30)28-14-17-3-7-27-8-4-17/h3-4,6-8,10-13,16,18,28H,5,9,14-15H2,1-2H3/t18-/m0/s1
Release date: 2019-05-29
Human protein kinase CK2 alpha in complex with CK2-TN03 (PDB entry 8C6N)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 336 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1785
R free: 0.2182
Average B factor: 29.4105
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 32% PEG4000, 0.2 M Lithium Sulfate
Matthews coefficient: 1.99
Solvent content (%): 38.34
Ligand: (2~{Z},5~{Z})-5-[(4-methoxy-3-oxidanyl-phenyl)methylidene]-2-phenylimino-1,3-thiazolidin-4-one (TN0)
Ligand formula: C17 H14 N2 O3 S
Ligand molecular weight: 326.37
Ligand SMILES: COc1ccc(cc1O)C=C2C(=O)NC(=Nc3ccccc3)S2
Ligand InChI: InChI=1S/C17H14N2O3S/c1-22-14-8-7-11(9-13(14)20)10-15-16(21)19-17(23-15)18-12-5-3-2-4-6-12/h2-10,20H,1H3,(H,18,19,21)/b15-10-
Release date: 2024-04-24
Crystal structure of HPK1 kinase domain T165E,S171E phosphomimetic mutant in complex with compound 9f (PDB entry 8XN7)
Macromolecule: Mitogen-activated protein kinase kinase kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 296 residues
Sequence: AMGSDVVDPDIFNRDPRDHYDLLQRLGGGTYGEVFKARDKVSGDLVALKMVKMEPDDDVSTLQKEILILKTCRHANIVAYHGSYLWLQKLWICMEFCGAGSLQDIYQVTGSLSELQISYVCREVLQGLAYLHSQKKIHRDIKGANILINDAGEVRLADFGISAQIGAELARRLEFIGTPYWMAPEVAAVALKGGYNELCDIWSLGITAIELAELQPPLFDVHPLRVLFLMTKSGYQPPRLKEKGKWSAAFHNFIKVTLTKSPKKRPSATKMLSHQLVSQPGLNRGLILDLLDKLKN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2144
R free: 0.2302
Average B factor: 49.62
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M sodium chloride, 0.1 M Tris, 
8%(w/v)PEG 20000, pH=8.0
Matthews coefficient: 2.45
Solvent content (%): 49.72
Ligand: 5-amino-2-((6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-yl)amino)-8-(2-(trifluoromethyl)benzyl)pyrido[2,3-d]pyrimidin-7(8H)-one (A1LVT)
Ligand formula: C26 H25 F3 N6 O2
Ligand molecular weight: 510.511
Ligand SMILES: CN1CCc2cc(c(cc2C1)Nc3ncc4c(n3)N(C(=O)C=C4N)Cc5ccccc5C(F)(F)F)OC
Ligand InChI: InChI=1S/C26H25F3N6O2/c1-34-8-7-15-10-22(37-2)21(9-17(15)13-34)32-25-31-12-18-20(30)11-23(36)35(24(18)33-25)14-16-5-3-4-6-19(16)26(27,28)29/h3-6,9-12H,7-8,13-14,30H2,1-2H3,(H,31,32,33)
Release date: 2024-04-10
BIO-2895 (BRD0705) bound GSK3beta-axin complex (PDB entry 7SXJ)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 351 residues
Sequence: GGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHAR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1838
R free: 0.2034
Average B factor: 47.94
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M calcium acetate, 0.1M BisTRIS pH 7.0, 5% Glycerol and 17% PEG3350
Matthews coefficient: 2.5
Solvent content (%): 50.72
Ligand: (4~{S})-4-ethyl-7,7-dimethyl-4-phenyl-2,6,8,9-tetrahydropyrazolo[3,4-b]quinolin-5-one (6VL)
Ligand formula: C20 H23 N3 O
Ligand molecular weight: 321.416
Ligand SMILES: CCC1(c2c[nH]nc2NC3=C1C(=O)CC(C3)(C)C)c4ccccc4
Ligand InChI: InChI=1S/C20H23N3O/c1-4-20(13-8-6-5-7-9-13)14-12-21-23-18(14)22-15-10-19(2,3)11-16(24)17(15)20/h5-9,12H,4,10-11H2,1-3H3,(H2,21,22,23)/t20-/m0/s1
Release date: 2023-06-14
Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor ATP (PDB entry 6ZJD)
Macromolecule: GTP:AMP phosphotransferase AK3, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.4.10
Sequence length: 227 residues
Sequence: MGASARLLRAVIMGAPGSGKGTVSSRITTHFELKHLSSGDLLRDNMLRGTEIGVLAKAFIDQGKLIPDDVMTRLALHELKNLTQYSWLLDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIKQRLTARWIHPASGRVYNIEFNPPKTVGIDDLTGEPLIQREDDKPETVIKRLKAYEDQTKPVLEYYQKKGVLETFSGTETNKIWPYVYAFLQTKVPQRSQKASVTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1568
R free: 0.2195
Average B factor: 19.8649
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Purified hAK3 was dialyzed against 30 mM MOPS buffer with 50 mM NaCl pH 7.0 and concentrated to 15-20 mg per ml. The resevoir contained 0.2 M MgCl2, 0.1 M Tris pH 8.0 and 20% PEG 6000. Drop size 1 plus 1 microliter. Cryo protection 30% PEG6000
Matthews coefficient: 2.46
Solvent content (%): 49.93
Ligand: ADENOSINE-5'-TRIPHOSPHATE (ATP)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2020-09-16