satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of 14-3-3 gamma in complex with caspase-2 14-3-3 binding motif Ser164 (PDB entry 6GKG)
Macromolecule: 14-3-3 protein gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 234 residues
Sequence: MVDREQLVQKARLAEQAERYDDMAAAMKNVTELNEPLSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTSADGNEKKIEMVRAYREKIEKELEAVCQDVLSLLDNYLIKNCSETQYESKVFYLKMKGDYYRYLAEVATGEKRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALNYSVFYYEIQNAPEQACHLAKTAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWT
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.847
R work: 0.2312
R free: 0.2871
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293.15
Crystal growth procedure: Tris-HCl, PEG 4000, lithium sulfate
Matthews coefficient: 2.6
Solvent content (%): 52.76
Release date: 2018-10-17
Dual specificity mitogen-activated protein kinase kinase 7 in complex with pyrazolopyrimidine 1a (PDB entry 6QHO)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 318 residues
Sequence: MGHHHHHHSAKQTGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTCAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGISGRLVDSKAKTRSAGCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTESPRTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2214
R free: 0.2809
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M soidumcitrate
20% PEG3350
Matthews coefficient: 2.77
Solvent content (%): 55.65
Ligand: 1-[(3~{R})-3-(4-azanylpyrazolo[3,4-d]pyrimidin-1-yl)piperidin-1-yl]propan-1-one (J3H)
Ligand formula: C13 H18 N6 O
Ligand molecular weight: 274.322
Ligand SMILES: CCC(=O)N1CCCC(C1)n2c3c(cn2)c(ncn3)N
Ligand InChI: InChI=1S/C13H18N6O/c1-2-11(20)18-5-3-4-9(7-18)19-13-10(6-17-19)12(14)15-8-16-13/h6,8-9H,2-5,7H2,1H3,(H2,14,15,16)/t9-/m1/s1
Release date: 2019-05-22
Crystal Structure of EGFR-T790M/V948R in Complex with Osimertinib and EAI045 (PDB entry 6Z4B)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 333 residues
Sequence: GSHMASGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2207
R free: 0.2513
Average B factor: 59.2924
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 27.5 % PEG3350, 100 mM MgSO4, 4 % ethylen glycole, 4.7 mg/mL EGFR-T790M/V948R (in 100 mM NaCl, 25 mM Tris-HCl, 10 % glycerol, 1 mM TCEP, pH 8.0) 1 ul reservoir + 1 ul protein solution)
Ligand: ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide (Q6K)
Ligand formula: C28 H35 N7 O2
Ligand molecular weight: 501.623
Ligand SMILES: CCC(=O)Nc1cc(c(cc1N(C)CCN(C)C)OC)Nc2nccc(n2)c3cn(c4c3cccc4)C
Ligand InChI: InChI=1S/C28H35N7O2/c1-7-27(36)30-22-16-23(26(37-6)17-25(22)34(4)15-14-33(2)3)32-28-29-13-12-21(31-28)20-18-35(5)24-11-9-8-10-19(20)24/h8-13,16-18H,7,14-15H2,1-6H3,(H,30,36)(H,29,31,32)
Release date: 2020-11-11
Human protein kinase CK2 alpha in complex with boldine (PDB entry 6HNY)
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): 1.65
R work: 0.1732
R free: 0.2063
Average B factor: 26.8921
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: 1.96
Solvent content (%): 37.35
Ligand: Boldine (GHT)
Ligand formula: C19 H19 N O4
Ligand molecular weight: 325.358
Ligand SMILES: CN1CCc2cc(c(c3c2c1cc4c3cc(c(c4)O)OC)OC)O
Ligand InChI: InChI=1S/C19H19NO4/c1-20-5-4-10-7-15(22)19(24-3)18-12-9-16(23-2)14(21)8-11(12)6-13(20)17(10)18/h6-9,21-22H,4-5H2,1-3H3
Release date: 2019-08-07
Development of a novel tricyclic class of potent and selective FIXa inhibitors (PDB entry 5EGM)
Macromolecule: Coagulation factor IX
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.22
Sequence length: 235 residues
Sequence: VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGASALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.841
R work: 0.148
R free: 0.1714
Average B factor: 34.6
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 295
Crystal growth procedure: 50 MM CHES, PH 9.0, 1.3 M TRI-SODIUM     
REMARK 280  CITRATE AND 3 MM COMPOUND (CROSS SEEDED WITH CRYSTALS GROWN FROM    
REMARK 280  50 MM TRIS, PH 7.2, 1.45 M AMMONIUM SULFATE, 2.0 M SODIUM           
REMARK 280  CHLORIDE AND 3 MM COMPOUND)
Matthews coefficient: 2.81
Solvent content (%): 56.17
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2015-11-18
Structure of human galactokinase in complex with galactose and 2'-(benzo[d]oxazol-2-ylamino)-7',8'-dihydro-1'H-spiro[cyclopentane-1,4'-quinazolin]-5'(6'H)-one (PDB entry 6ZFH)
Macromolecule: Galactokinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.6
Sequence length: 399 residues
Sequence: MAHHHHHHAALRQPQVAELLAEARRAFREEFGAEPELAVSAPGRVNLIGEHTDYNQGLVLPMALELMTVLVGSPRKDGLVSLLTTSEGADEPQRLQFPLPTAQRSLEPGTPRWANYVKGVIQYYPAAPLPGFSAVVVSSVPLGGGLSSSASLEVATYTFLQQLCPDSGTIAARAQVCQQAEHSFAGMPCGIMDQFISLMGQKGHALLIDCRSLETSLVPLSDPKLAVLITNSNVRHSLASSEYPVRRRQCEEVARALGAASLREVQLEELEAARDLVSKEGFRRARHVVGEIRRTAQAAAALRRGDYRAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMTGGGFGGCTVTLLEASAAPHAMRHIQEHYGGTATFYLSQAADGAKVLCL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.439
R work: 0.2097
R free: 0.2619
Average B factor: 58.6014
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Morpheus condition:

Buffer system 1:
0.1 M pH 6.5, Imidazole; MES monohydrate (acid)

Amino acids:
0.02M L-Na-Glutamate; 0.02M Alanine (racemic); 0.02M Glycine; 0.02M Lysine HCl (racemic); 0.02M Serine (racemic)

Precipitant Mix 1:
20% v/v PEG 500 MME; 10 % w/v PEG 20000
Matthews coefficient: 2.42
Solvent content (%): 49.17
Ligand: beta-D-galactopyranose (GAL)
Ligand formula: C6 H12 O6
Ligand molecular weight: 180.156
Ligand SMILES: C(C1C(C(C(C(O1)O)O)O)O)O
Ligand InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4+,5-,6-/m1/s1
Release date: 2021-06-30
STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A PYRROLIDINE-3-CARBOXYLIC ACID FRAGMENT 587 (PDB entry 6YV0)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2114
R free: 0.2343
Average B factor: 47.18
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 295
Crystal growth procedure: 1.4 M AMMONIUM SULPHATE, 0.1 M CITRIC ACID, PH 4.0
Matthews coefficient: 1.96
Solvent content (%): 37.4
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: 2020-05-13
Crystal structure of the R178Q mutant of ubiquitin carboxy terminal hydrolase L1 (UCH-L1) (PDB entry 8DY8)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase isozyme L1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 228 residues
Sequence: GPLGSMQLKPMEINPEMLNKVLSRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDGSVLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGQMPFPVNHGASSEDTLLKDAAKVCREFTEREQGEVRFSAVALCKAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2218
R free: 0.2645
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: 2.4 M Ammonium Sulfate, 0.1 M HEPES
Matthews coefficient: 2.35
Solvent content (%): 47.59
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: 2023-08-09
HUMAN PI3KDELTA IN COMPLEX WITH PYRIDAZINONE INHIBITOR 7 (PDB entry 8S3R)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.137
Sequence length: 1018 residues
Sequence: NQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPEAYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYSFPLQLEPSAQTWGPGTLRLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKATVFRQPLVEQPEDYTLQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNPAPQVQKPRAKPPPIPAKKPSSVSLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKAKKARSTKKKSKKADCPIAWANLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAPHPVYYPALEKILELGRHSECVHVTEEEQLQLREILERRGSGELYEHEKDLVWKLRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLDRALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEALSHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEAGSGGSVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLNKSNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNFKTKFGINRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRESWKTKVNWL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.20308
R free: 0.26963
Average B factor: 74.287
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG6000, 0.10 M KCL, 0.10 M MES
Matthews coefficient: 2.53
Solvent content (%): 51.36
Ligand: 5-[(1~{S})-1-[4-azanyl-3-(5-oxidanylpyridin-3-yl)pyrazolo[3,4-d]pyrimidin-1-yl]ethyl]-4-cyclopentyl-2-(phenylmethyl)pyridazin-3-one (A1H48)
Ligand formula: C28 H28 N8 O2
Ligand molecular weight: 508.574
Ligand SMILES: CC(C1=C(C(=O)N(N=C1)Cc2ccccc2)C3CCCC3)n4c5c(c(n4)c6cc(cnc6)O)c(ncn5)N
Ligand InChI: InChI=1S/C28H28N8O2/c1-17(36-27-24(26(29)31-16-32-27)25(34-36)20-11-21(37)13-30-12-20)22-14-33-35(15-18-7-3-2-4-8-18)28(38)23(22)19-9-5-6-10-19/h2-4,7-8,11-14,16-17,19,37H,5-6,9-10,15H2,1H3,(H2,29,31,32)/t17-/m0/s1
Release date: 2024-07-03
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z28290384 (PDB entry 5RW8)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.27
R work: 0.1752
R free: 0.1948
Average B factor: 17.017
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.11
Solvent content (%): 41.63
Ligand: N-(2-fluorophenyl)-3-methoxybenzamide (WN1)
Ligand formula: C14 H12 F N O2
Ligand molecular weight: 245.249
Ligand SMILES: COc1cccc(c1)C(=O)Nc2ccccc2F
Ligand InChI: InChI=1S/C14H12FNO2/c1-18-11-6-4-5-10(9-11)14(17)16-13-8-3-2-7-12(13)15/h2-9H,1H3,(H,16,17)
Release date: 2020-11-11
Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (cr) (PDB entry 7MXS)
Macromolecule: Exonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 358 residues
Sequence: MGIQGLLQFIKEASEPIHVRKYKGQVVAVDTYCWLHKGAIACAEKLAKGEPTDRYVGFCMKFVNMLLSHGIKPILVFDGCTLPSKKEVERSRRERRQANLLKGKQLLREGKVSEARECFTRSINITHAMAHKVIKAARSQGVDCLVAPYEADAQLAYLNKAGIVQAIITEDSDLLAFGCKKVILKMDQFGNGLEIDQARLGMCRQLGDVFTEEKFRYMCILSGCDYLSSLRGIGLAKACKVLRLANNPDIVKVIKKIGHYLKMNITVPEDYINGFIRANNTFLYQLVFDPIKRKLIPLNAYEDDVDPETLSYAGQYVDDSIALQIALGNKDINTFEQIDDYNPDTAMPAHSRENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.798
R work: 0.2127
R free: 0.2473
Average B factor: 99.5807
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 290
Crystal growth procedure: 100 mM sodium acetate, pH 7.0; 10 mM KCl; 2-4% PEG 4000
Matthews coefficient: 2.59
Solvent content (%): 52.48
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: 2023-05-10
Human DNA Ligase 1 - R771W nicked DNA complex (PDB entry 7L35)
Macromolecule: DNA ligase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.5.1.1
Sequence length: 647 residues
Sequence: SNDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLELGVGDGVLLKAVAQATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFRDIARLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKWAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQNQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1626
R free: 0.1948
Average B factor: 40.6345
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, pH 6, 100 mM lithium acetate, 15% (w/v) polyethylene glycol PEG3350
Matthews coefficient: 2.5
Solvent content (%): 50.77
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2021-01-13
Crystal structure of the p300 acetyltransferase domain with peptide-competitive inhibitor 2 (PDB entry 6V8K)
Macromolecule: Histone acetyltransferase p300
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 323 residues
Sequence: GSKFSAKRLPSTRLGTFLENRVNDFLRRQNHPESGEVTVRVVHASDKTVEVKPGMKARFVDSGEMAESFPYRTKALFAFEEIDGVDLCFFGMHVQEYGSDCPPPNQRRVYISYLDSVHFFRPKCLRTAVYHEILIGYLEYVKKLGYTTGHIWACPPSEGDDYIFHCHPPDQKIPKPKRLQEWFKKMLDKAVSERIVHDYKDIFKQATEDRLTSAKELPYFEGDFWPNVLEESIKESGGSGSQKLYATMEKHKEVFFVIRLIAGPAANSLPPIVDPDPLIPCDLMDGRDAFLTLARDKHLEFSSLRRAQWSTMCMLVELHTQSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1786
R free: 0.2134
Average B factor: 45.88
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.24 mM HAT, 0.12 mM CoA, 0.75 mM ligand. 200+150 (+20) nL sitting drops.
Internal focus screen with microseeding. 17.5% MPD, 0.1 M Tris pH 8, 2.5 % PEG3350. Cryo 30% MPD, 5% PEG 3350, 1 mM ligand
Matthews coefficient: 2.49
Solvent content (%): 50.61
Ligand: 1-(2-methyl-1H-indol-3-yl)-2-[(2R)-2-methylpiperidin-1-yl]ethan-1-one (QS4)
Ligand formula: C17 H22 N2 O
Ligand molecular weight: 270.369
Ligand SMILES: Cc1c(c2ccccc2[nH]1)C(=O)CN3CCCCC3C
Ligand InChI: InChI=1S/C17H22N2O/c1-12-7-5-6-10-19(12)11-16(20)17-13(2)18-15-9-4-3-8-14(15)17/h3-4,8-9,12,18H,5-7,10-11H2,1-2H3/t12-/m1/s1
Release date: 2020-04-01
Crystal structure of human phosphatase PTEN treated with a bisperoxovanadium complex (PDB entry 5BZX)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 314 residues
Sequence: RRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVMICAYLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEEDNDKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1752
R free: 0.2037
Average B factor: 59.842
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 6.5, 1.25 M L-tartrat, 7.5% glycerol
Matthews coefficient: 3.15
Solvent content (%): 60.9
Ligand: VANADATE ION (VO4)
Ligand formula: O4 V
Ligand molecular weight: 114.939
Ligand SMILES: [O-][V](=O)([O-])[O-]
Ligand InChI: InChI=1S/4O.V/q;3*-1;
Release date: 2015-10-07
Human tnik in complex with compound 9 (PDB entry 6RA7)
Macromolecule: TRAF2 and NCK-interacting protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 306 residues
Sequence: GSDEIDLSALRDPAGIFELVELVGNGTYGQVYKGRHVKTGQLAAIKVMDVTGDEEEEIKQEINMLKKYSHHRNIATYYGAFIKKNPPGMDDQLWLVMEFCGAGSVTDLIKNTKGNTLKEEWIAYICREILRGLSHLHQHKVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATYDFKSDLWSLGITAIEMAEGAPPLCDMHPMRALFLIPRNPAPRLKSKKWSKKFQSFIESCLVKNHSQRPATEQLMKHPFIRDQPNERQVRIQLKDHIDRTKKKRG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG3350 w/v, 0.1M PCTP (pH 8.0), 200 mM sodium formate w/v
Matthews coefficient: 2.39
Solvent content (%): 48.57
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: 2019-11-06
Crystal Structure of Drosophila DHX36 helicase in complex with TAGGGTTTT (PDB entry 5N98)
Macromolecule: DNA (5'-D(P*TP*AP*GP*GP*GP*TP*TP*TP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 9 residues
Sequence: TAGGGTTTT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.756
R work: 0.1746
R free: 0.2365
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M MES monohydrate-imidazole
20mM sodium formate
20mM ammonium acetate
20mM sodium citrate tribasic hydrate
20mM sodium oxamate
20mM potassium sodium tartrate tetrahydrat
Matthews coefficient: 2.69
Solvent content (%): 53.49
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2018-03-14
Human Butyrylcholinesterase in complex with ((S)-2-(butylamino)-N-(2-(4-(dimethylamino)cyclohexyl)ethyl)-3-(1H-indol-3-yl)propanamide (PDB entry 6QAD)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 557 residues
Sequence: MDSKVTIICIRFLFWFLLLCMLIGKSHTEDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.497
R work: 0.1998
R free: 0.2344
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate
MES pH 6.5
Matthews coefficient: 3.14
Solvent content (%): 60.85
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: 2019-03-27