satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human low molecular weight protein tyrosine phosphatase (LMPTP) type A complexed with MES (PDB entry 5JNT)
Macromolecule: Low molecular weight phosphotyrosine protein phosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 160 residues
Sequence: GSMAEQVTKSVLFVCLGNICRSPIAEAVFRKLVTDQNISENWRVDSAATSGYEIGNPPDYRGQSCMKRHGIPMSHVARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSDFETVYQQCVRCCRAFLEKAH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1346
R free: 0.1658
Average B factor: 15.964
Crystallization method: EVAPORATION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 200 mM NaCl, 40 mM MES
Matthews coefficient: 2.47
Solvent content (%): 50.11
Ligand: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID (MES)
Ligand formula: C6 H13 N O4 S
Ligand molecular weight: 195.237
Ligand SMILES: C1COCC[NH+]1CCS(=O)(=O)[O-]
Ligand InChI: InChI=1S/C6H13NO4S/c8-12(9,10)6-3-7-1-4-11-5-2-7/h1-6H2,(H,8,9,10)
Release date: 2017-03-29
Crystal structure of tyrosine-protein kinase SYK with an inhibitor (PDB entry 4RSS)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 290 residues
Sequence: EEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNLEHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.21189
R free: 0.24869
Average B factor: 32.173
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 10-20% (v/v) PEG 3350, 100mM Tris-HCl (pH 8.5) 
, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2.12
Solvent content (%): 42.11
Ligand: 1-[(3-methyl-1-{2-[(1,2,3-trimethyl-1H-indol-5-yl)amino]pyrimidin-4-yl}-1H-pyrazol-4-yl)methyl]azetidin-3-ol (4MG)
Ligand formula: C23 H27 N7 O
Ligand molecular weight: 417.507
Ligand SMILES: Cc1c(n(c2c1cc(cc2)Nc3nccc(n3)n4cc(c(n4)C)CN5CC(C5)O)C)C
Ligand InChI: InChI=1S/C23H27N7O/c1-14-16(3)28(4)21-6-5-18(9-20(14)21)25-23-24-8-7-22(26-23)30-11-17(15(2)27-30)10-29-12-19(31)13-29/h5-9,11,19,31H,10,12-13H2,1-4H3,(H,24,25,26)
Release date: 2015-10-21
Crystal structure of an inhibitor-bound Syk (PDB entry 4XG9)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 290 residues
Sequence: EEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNLEHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.91
R work: 0.2085
R free: 0.24104
Average B factor: 49.781
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 278
Crystal growth procedure: 10~20%(v/v) PEG3350, 100 mM Tris-HCl
Matthews coefficient: 2.12
Solvent content (%): 41.85
Ligand: 1-[(1-{2-[(3-chloro-1,2-dimethyl-1H-indol-5-yl)amino]pyrimidin-4-yl}-3-methyl-1H-pyrazol-4-yl)methyl]azetidin-3-ol (X9G)
Ligand formula: C22 H24 Cl N7 O
Ligand molecular weight: 437.925
Ligand SMILES: Cc1c(cn(n1)c2ccnc(n2)Nc3ccc4c(c3)c(c(n4C)C)Cl)CN5CC(C5)O
Ligand InChI: InChI=1S/C22H24ClN7O/c1-13-15(9-29-11-17(31)12-29)10-30(27-13)20-6-7-24-22(26-20)25-16-4-5-19-18(8-16)21(23)14(2)28(19)3/h4-8,10,17,31H,9,11-12H2,1-3H3,(H,24,25,26)
Release date: 2015-12-30
Crystal structure of hMTH1 F27A in complex with LW14 in the absence of acetate (PDB entry 6GLH)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 182 residues
Sequence: MKHHHHHHPMSDYDIPTTENLYFQGAMGASRLYTLVLVLQPQRVLLGMKKRGAGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.201
R work: 0.1935
R free: 0.2014
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: crystallized in: 23-27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5

soaked in: 0.27 M ammonium sulfate, 17% glycerol, 27% PEG4000, 20% DMSO, 10 mM compound
Matthews coefficient: 1.72
Solvent content (%): 28.54
Ligand: 1~{H}-imidazo[4,5-b]pyridin-2-amine (BU8)
Ligand formula: C6 H6 N4
Ligand molecular weight: 134.139
Ligand SMILES: c1cc2c(nc1)nc([nH]2)N
Ligand InChI: InChI=1S/C6H6N4/c7-6-9-4-2-1-3-8-5(4)10-6/h1-3H,(H3,7,8,9,10)
Release date: 2019-02-20
Human thrombin sandwiched between two DNA aptamers: HD22 and HD1-deltaT3 (PDB entry 5EW1)
Macromolecule: thrombin light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.1555
R free: 0.208
Average B factor: 50.954
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 28% MPEG 2000, 
0.1 M Bis/Tris pH 6.5
Matthews coefficient: 2.73
Solvent content (%): 55.02
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: 2016-11-30
Crystal Structure of Factor VIIa in complex with 1-(1-aminoisoquinolin-6-yl)-3-benzylurea (PDB entry 5PAJ)
Macromolecule: Coagulation factor VII light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 64 residues
Sequence: LICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEKRNASKPQGR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2
R free: 0.2241
Average B factor: 24.376
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol
Ligand: 1-(1-azanylisoquinolin-6-yl)-3-(phenylmethyl)urea (7XJ)
Ligand formula: C17 H16 N4 O
Ligand molecular weight: 292.335
Ligand SMILES: c1ccc(cc1)CNC(=O)Nc2ccc3c(c2)ccnc3N
Ligand InChI: InChI=1S/C17H16N4O/c18-16-15-7-6-14(10-13(15)8-9-19-16)21-17(22)20-11-12-4-2-1-3-5-12/h1-10H,11H2,(H2,18,19)(H2,20,21,22)
Release date: 2017-06-21
Crystal structure of human legumain (AEP) in complex with compound 11b (PDB entry 5LUA)
Macromolecule: Legumain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.34
Sequence length: 262 residues
Sequence: GGKHWVVIVAGSNGWYNYRHQADACHAYQIIHRNGIPDEQIVVMMYDDIAYSEDNPTPGIVINRPNGTDVYQGVPKDYTGEDVTPQNFLAVLRGDAEAVKGIGSGKVLKSGPQDHVFIYFTNHGSTGILVFPNEDLHVKDLNETIHYMYKHKMYRKMVFYIEACESGSMMNHLPDNINVYATTAANPRESSYACYYDEKRSTYLGDWYSVNWMEDSDVEDLTKETLHKQYHLVKSHTQTSHVMQYGNKTISTMKVMQFQGMK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.222
R free: 0.252
Average B factor: 27.4
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 22 % PEG 3350, 0.1 M sodium acetate pH 4.5
Matthews coefficient: 2.34
Solvent content (%): 47.41
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: 2017-03-29
Meta-Nidocarborane propyl-sulfonamide in complex with CA IX mimic (PDB entry 6YOL)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.15
R work: 0.1409
R free: 0.1705
Average B factor: 18.945
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: 2.11
Solvent content (%): 41.58
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: 2020-08-19
Protein kinase MKK7 in complex with difluoro-phenethyltriazole-substituted pyrazolopyrimidine (PDB entry 7OVJ)
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: MGHHHHHHSAKQTGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTCAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGISGRLVDSKAKTRSAGCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTRSPRTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.2017
R free: 0.2445
Average B factor: 57.81
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 180-220 mM sodium citrate,
15-25 % PEG3350
Matthews coefficient: 2.42
Solvent content (%): 49.08
Ligand: 1-[(3~{R})-3-[4-azanyl-3-[1-[2,2-bis(fluoranyl)-2-phenyl-ethyl]-1,2,3-triazol-4-yl]pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one (24N)
Ligand formula: C23 H25 F2 N9 O
Ligand molecular weight: 481.501
Ligand SMILES: CCC(=O)N1CCCC(C1)n2c3c(c(n2)c4cn(nn4)CC(c5ccccc5)(F)F)c(ncn3)N
Ligand InChI: InChI=1S/C23H25F2N9O/c1-2-18(35)32-10-6-9-16(11-32)34-22-19(21(26)27-14-28-22)20(30-34)17-12-33(31-29-17)13-23(24,25)15-7-4-3-5-8-15/h3-5,7-8,12,14,16H,2,6,9-11,13H2,1H3,(H2,26,27,28)/t16-/m1/s1
Release date: 2022-07-20
Caspase-3 Mutant - D9A,D28A,S150D (PDB entry 6BG0)
Macromolecule: Caspase-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.56
Sequence length: 175 residues
Sequence: MENTENSVASKSIKNLEPKIIHGSESMASGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRDLTGKPKLFIIQACRGTELDCGIETD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.125
R work: 0.1606
R free: 0.2011
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
Matthews coefficient: 2.26
Solvent content (%): 45.53
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-02-21
Crystal structure of human MTH1 in complex with O6-methyl-dGMP (PDB entry 5OTM)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 159 residues
Sequence: GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.19612
R free: 0.24688
Average B factor: 24.366
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 3.7
Crystallization temperature (K): 293
Crystal growth procedure: 26% w/v PEG6000, 0.1 M Sodium acetate trihydrate pH 3.7, 0.2 M LiSO4, 3 mM O6-methyl-2'-dGTP, 2 mM TCEP
Matthews coefficient: 2.17
Solvent content (%): 43.26
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2018-09-05
Carbonic Anhydrase II complexed with 4-(2-(3-(4-methylphenyl)ureido)ethylsulfonamido)benzenesulfonamide (PDB entry 7K6J)
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): 1.755
R work: 0.1868
R free: 0.2177
Average B factor: 19.163
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 295
Crystal growth procedure: 1.6M Sodium Citrate, 50mM Tris, pH 6.4
Matthews coefficient: 2.11
Solvent content (%): 41.61
Ligand: 4-{[(2-{[(4-methylphenyl)carbamoyl]amino}ethyl)sulfonyl]amino}benzene-1-sulfonamide (VYY)
Ligand formula: C16 H20 N4 O5 S2
Ligand molecular weight: 412.484
Ligand SMILES: Cc1ccc(cc1)NC(=O)NCCS(=O)(=O)Nc2ccc(cc2)S(=O)(=O)N
Ligand InChI: InChI=1S/C16H20N4O5S2/c1-12-2-4-13(5-3-12)19-16(21)18-10-11-26(22,23)20-14-6-8-15(9-7-14)27(17,24)25/h2-9,20H,10-11H2,1H3,(H2,17,24,25)(H2,18,19,21)
Release date: 2020-12-23
Structure of human DPP3 in complex with opioid peptide leu-enkephalin (PDB entry 5E3A)
Macromolecule: Dipeptidyl peptidase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.14.4
Sequence length: 726 residues
Sequence: MADTQYILPNDIGVSSLDSREAFRLLSPTERLYAYHLSRAAWYGGLAVLLQTSPEAPYIYALLSRLFRAQDPDQLRQHALAEGLTEEEYQAFLVYAAGVYSNMGNYKSFGDTKFVPNLPKEKLERVILGSEAAQQHPEEVRGLWQTCGELMFSLEPRLRHLGLGKEGITTYFSGNCTMEDAKLAQDFLDSQNLSAYNTRLFKEVDGCGKPYYEVRLASVLGSEPSLDSEVTSKLKSYEFRGSPFQVTRGDYAPILQKVVEQLEKAKAYAANSHQGQMLAQYIESFTQGSIEAHKRGSRFWIQDKGPIVESYIGFIESYRDPFGSRGEFEGFVAVVNKAMSAKFERLVASAEQLLKELPWPPTFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPNYDDLRQTEGFKNVSLGNVLAVAYATQREKLTFLEEDDKDLYILWKGPSFDVQVGLHALLGHGSGKLFVQDEKGAFNFDQETVINPETGEQIQSWYRCGETWDSKFSTIASSYEECRAESVGLYLSLHPQVLEIFGFEGADAEDVIYVNWLNMVRAGLLALEFYTPEAFNWRQAHMQARFVILRVLLEAGEGLVTITPTTGSDGRPDARVRLDRSKIRSVGKPALERFLRRLQVLKSTGDVAGGRALYEGYATVTDAPPESFLTLRDTVLLRKESRKLIVQPNTRLEGSDVQLLEYEASAAGLIRSFSERFPEDGPELEEILTQLATADARFW
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2088
R free: 0.2599
Average B factor: 37.2
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.056M SODIUM PHOSPHATE MONOBASIC MONOHYDRATE, 1.344M POTASSIUM PHOSPHATE DIBASIC
Matthews coefficient: 2.5
Solvent content (%): 50.82
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: 2016-04-13
APE1 exonuclease substrate complex with 8oxoG opposite C (PDB entry 7SVB)
Macromolecule: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 10 residues
Sequence: GCTGATGCGG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.1997
R free: 0.2452
Average B factor: 42.98
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 293.15
Crystal growth procedure: 7 - 14% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Matthews coefficient: 2.65
Solvent content (%): 53.5
Release date: 2022-09-07
MST3 IN COMPLEX WITH Danusertib (PDB entry 4QO9)
Macromolecule: SERINE/THREONINE-PROTEIN KINASE 24
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 310 residues
Sequence: GPLGSEFMAHSPVQSGLPGMQNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHSEKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKVLFLIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDRYKRWKAEQSHDDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1604
R free: 0.2183
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 12.5 mg/mL MST3, 1 mM Danusertib, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 2.15
Solvent content (%): 42.67
Ligand: TRIETHYLENE GLYCOL (PGE)
Ligand formula: C6 H14 O4
Ligand molecular weight: 150.173
Ligand SMILES: C(COCCOCCO)O
Ligand InChI: InChI=1S/C6H14O4/c7-1-3-9-5-6-10-4-2-8/h7-8H,1-6H2
Release date: 2015-07-29
Crystal structure of human NEIL1(R242) bound to duplex DNA containing a C:T mismatch (PDB entry 6LWQ)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 295 residues
Sequence: MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGRGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.89
R work: 0.2372
R free: 0.2828
Average B factor: 80.78
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000
Matthews coefficient: 2.81
Solvent content (%): 56.25
Release date: 2021-06-09
Crystal Structure of human cyclic GMP-AMP synthase in complex with 2-[[2-chloro-5-(1-methylpyrazol-3-yl)phenyl]methylamino]-5-(2-phenylethyl)-4H-[1,2,4]triazolo[1,5-a]pyrimidin-7-one (PDB entry 7FUE)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.169
R work: 0.2059
R free: 0.2696
Average B factor: 96.5576
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals
Matthews coefficient: 2.58
Solvent content (%): 52.31
Ligand: (8S)-2-({[(5P)-2-chloro-5-(1-methyl-1H-pyrazol-3-yl)phenyl]methyl}amino)-5-(2-phenylethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7(4H)-one (YQC)
Ligand formula: C24 H22 Cl N7 O
Ligand molecular weight: 459.931
Ligand SMILES: Cn1ccc(n1)c2ccc(c(c2)CNc3nc4n(n3)C(=O)C=C(N4)CCc5ccccc5)Cl
Ligand InChI: InChI=1S/C24H22ClN7O/c1-31-12-11-21(29-31)17-8-10-20(25)18(13-17)15-26-23-28-24-27-19(14-22(33)32(24)30-23)9-7-16-5-3-2-4-6-16/h2-6,8,10-14H,7,9,15H2,1H3,(H2,26,27,28,30)
Release date: 2024-02-21
Structure of LRRK2-CHK1 10-pt. mutant complex with heteroaryl-1H-indazole LRRK2 inhibitor 14 (PDB entry 8E80)
Macromolecule: Serine/threonine-protein kinase Chk1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICILKMLNHENVIKFYGHRREGNIQYLFMELASGGSLFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPHNLLLDERDNLKIADYSLATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRPRVTSGGVSESPSGHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.207
R free: 0.242
Average B factor: 26.95
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 11% PEG 8000, 15-20% ethylene glycol, 0.1 M MES (pH 6.5), 5% 6-aminohexanoic acid
Matthews coefficient: 2.36
Solvent content (%): 47.96
Ligand: 2-[(1r,4r)-2-{(6P)-6-[(6M)-6-(1H-pyrazol-5-yl)-1H-indazol-1-yl]pyrimidin-4-yl}-2-azabicyclo[2.1.1]hexan-4-yl]propan-2-ol (UUF)
Ligand formula: C22 H23 N7 O
Ligand molecular weight: 401.464
Ligand SMILES: CC(C)(C12CC(C1)N(C2)c3cc(ncn3)n4c5cc(ccc5cn4)c6ccn[nH]6)O
Ligand InChI: InChI=1S/C22H23N7O/c1-21(2,30)22-9-16(10-22)28(12-22)19-8-20(24-13-23-19)29-18-7-14(17-5-6-25-27-17)3-4-15(18)11-26-29/h3-8,11,13,16,30H,9-10,12H2,1-2H3,(H,25,27)/t16-,22-
Release date: 2023-02-22
Crystal structure of the PI3KC2alpha C2 domain in complex with IP6 (PDB entry 6BU0)
Macromolecule: Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.154
Sequence length: 131 residues
Sequence: SNAIGGAVKLSISYRNGTLFIMVMHIKDLVTEDGADPNPYVKTYLLPDNHKTSKRKTKISRKTRNPTFNEMLVYSGYSKETLRQRELQLSVLSAESLRGNFFLGGVTLPLKDFNLSKETVKWYQLTAATYL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.427
R work: 0.2094
R free: 0.2501
Average B factor: 58.7087
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: PEG 8000
Matthews coefficient: 2.52
Solvent content (%): 51.1
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2018-10-17