satarupa22/MacromolecularLigandDB huggingface dataset:
Fragment-based discovery of a highly potent, orally bioavailable inhibitor which modulates the phosphorylation and catalytic activity of ERK1/2 (PDB entry 6G92)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.164
R free: 0.227
Average B factor: 33.173
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M (NH4)2SO4, 0.1M HEPES/NaOHpH=7.2, 34.0%w/v MPEG 2000, 0.02M Mercaptoethanol
Matthews coefficient: 2.32
Solvent content (%): 46.91
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: 2018-05-30
The structure of human CamKII with bound inhibitor (PDB entry 5VLO)
Macromolecule: Calcium/calmodulin-dependent protein kinase type II subunit delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 302 residues
Sequence: GHMSTTTCTRFTDEYQLFEELGKGAFSVVRRCMKIPTGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGFHYLVFDLVTGGELFEDIVAREYYSEADASHCIQQILESVNHCHLNGIVHRDLKPENLLLASKSKGAAVKLADFGLAIEVQGDQQAWFGFAGTPGYLSPEVLRKDPYGKPVDMWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPAKRITASEALKHPWICQRSTVASMMHRQETVDCLKKFNARRKLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1828
R free: 0.2261
Average B factor: 41.0908881426
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 uL aliquots.   The protein was thawed and diluted down to 12 mg/mL in the same buffer just prior to crystallization experiments.  Sitting drop vapor diffusion droplets were assembled with 250 nL of 12 mg/mL CamKII, 0.6 mM inhibitor and 250 nL of reservoir solution 24% peg 3350, 0.2 M ammonium tartrate, 0.1 M arginine.   Flat crystal plates (typically 0.03 mm x 0.2 mm x 0.4 mm in size) grew in 4-7 days at 20 C.   A crystal seed suspension was prepared with ten crushed crystals combined into 100 uL of reservoir solution and stored at -80 C.  A thirty fold seed dilution was prepared in the same solution for addition to protein droplets in a 1 to 1 volume ratio to enhance crystallization of difficult to crystallize inhibitors.
Matthews coefficient: 2.35
Solvent content (%): 47.64
Ligand: N-[(2S)-2-(diethylamino)propyl]-2-[(2S)-2-(methylcarbamoyl)azetidin-1-yl]-6-[5-(thiophen-2-yl)pyrazolo[1,5-a]pyrimidin-3-yl]pyridine-4-carboxamide (9EJ)
Ligand formula: C28 H34 N8 O2 S
Ligand molecular weight: 546.687
Ligand SMILES: CCN(CC)C(C)CNC(=O)c1cc(nc(c1)N2CCC2C(=O)NC)c3cnn4c3nc(cc4)c5cccs5
Ligand InChI: InChI=1S/C28H34N8O2S/c1-5-34(6-2)18(3)16-30-27(37)19-14-22(32-25(15-19)35-11-10-23(35)28(38)29-4)20-17-31-36-12-9-21(33-26(20)36)24-8-7-13-39-24/h7-9,12-15,17-18,23H,5-6,10-11,16H2,1-4H3,(H,29,38)(H,30,37)/t18-,23-/m0/s1
Release date: 2017-08-23
Crystal structure of a P38alpha T185G mutant in complex with TAB1 peptide. (PDB entry 5O90)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGHRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVAGRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLAQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.49
R work: 0.249
R free: 0.2748
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG3350
0.2M Na/K Tartrate
0.1M pH7.0 Bis-Tris Propane
Matthews coefficient: 2.24
Solvent content (%): 45.12
Ligand: 4-(4-FLUOROPHENYL)-1-(4-PIPERIDINYL)-5-(2-AMINO-4-PYRIMIDINYL)-IMIDAZOLE (SB4)
Ligand formula: C18 H19 F N6
Ligand molecular weight: 338.382
Ligand SMILES: c1cc(ccc1c2c(n(cn2)C3CCNCC3)c4ccnc(n4)N)F
Ligand InChI: InChI=1S/C18H19FN6/c19-13-3-1-12(2-4-13)16-17(15-7-10-22-18(20)24-15)25(11-23-16)14-5-8-21-9-6-14/h1-4,7,10-11,14,21H,5-6,8-9H2,(H2,20,22,24)
Release date: 2018-01-31
Crystal Structure of Aurora-A L210C catalytic domain in complex with ASDO2 (PDB entry 6HJK)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 285 residues
Sequence: GAMESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLICEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPSNAQNKESASKQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2169
R free: 0.2523
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.2 M ammonium sulfate, 0.1 M tri-sodium citrate pH 5.6, 25 % w/v polyethylene glycol 4000
Matthews coefficient: 2.67
Solvent content (%): 54
Ligand: (~{E})-~{N}-[4-(4-azanyl-1-propan-2-yl-pyrazolo[3,4-d]pyrimidin-3-yl)phenyl]-4-[4-fluoranyl-3-(trifluoromethyl)phenyl]-4-oxidanylidene-but-2-enamide (G7W)
Ligand formula: C25 H20 F4 N6 O2
Ligand molecular weight: 512.459
Ligand SMILES: CC(C)n1c2c(c(n1)c3ccc(cc3)NC(=O)C=CC(=O)c4ccc(c(c4)C(F)(F)F)F)c(ncn2)N
Ligand InChI: InChI=1S/C25H20F4N6O2/c1-13(2)35-24-21(23(30)31-12-32-24)22(34-35)14-3-6-16(7-4-14)33-20(37)10-9-19(36)15-5-8-18(26)17(11-15)25(27,28)29/h3-13H,1-2H3,(H,33,37)(H2,30,31,32)/b10-9+
Release date: 2018-10-03
Crystal structure of ERK2 covalently bound to SM1-71 (PDB entry 6G54)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 361 residues
Sequence: SMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.18322
R free: 0.22096
Average B factor: 55.794
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.9
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.9M Li2SO4 and 0.1M citrate 5.9
Matthews coefficient: 2.91
Solvent content (%): 57.66
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: 2019-02-27
Crystal structure of human PI3K-gamma in complex with inhibitor IPI-549 (PDB entry 6XRL)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 949 residues
Sequence: MSEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVTSKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDTPGAILQSFFTKMAKKKSLMDIPESQSEQDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRKEEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRNTDLTVFVEANIQHGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSSKASAESPSSESKGKVQLLYYVNLLLIDHRFLLRRGEYVLHMWQISGKGEDQGSFNADKLTSATNPDKENSMSISILLDNYCHPIALPKHQPTPDPEGDRVRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKHPKAYPKLFSSVKWGQQEIVAKTYQLLARREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIEMLQKVTLDIKSLSAEKYDVSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLNHWLKEKSPTEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKNEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.99
R work: 0.2023
R free: 0.2694
Average B factor: 127.957
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: PEG 4000,  (NH4)2SO4, Na Form, Tris
Matthews coefficient: 2.51
Solvent content (%): 51.07
Ligand: 2-amino-N-[(1S)-1-{8-[(1-methyl-1H-pyrazol-4-yl)ethynyl]-1-oxo-2-phenyl-1,2-dihydroisoquinolin-3-yl}ethyl]pyrazolo[1,5-a]pyrimidine-3-carboxamide (V7Y)
Ligand formula: C30 H24 N8 O2
Ligand molecular weight: 528.564
Ligand SMILES: CC(C1=Cc2cccc(c2C(=O)N1c3ccccc3)C#Cc4cnn(c4)C)NC(=O)c5c(nn6c5nccc6)N
Ligand InChI: InChI=1S/C30H24N8O2/c1-19(34-29(39)26-27(31)35-37-15-7-14-32-28(26)37)24-16-22-9-6-8-21(13-12-20-17-33-36(2)18-20)25(22)30(40)38(24)23-10-4-3-5-11-23/h3-11,14-19H,1-2H3,(H2,31,35)(H,34,39)/t19-/m0/s1
Release date: 2020-09-16
LSD1-CoREST in complex with T108 and SNAG peptide (PDB entry 8FJ7)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.66
Sequence length: 871 residues
Sequence: GSSHHHHHHSSGLVPRGSHMLSGKKAAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERTPRKKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGRRTSRRKRAKVEYREMDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAPPEEENESEPEEPSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTLPRQATPGVPAQQSPSM
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2217
R free: 0.2427
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Matthews coefficient: 5.6
Solvent content (%): 78
Ligand: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[7,8-dimethyl-2,4-dioxo-5-{3-[3-(phenylcarbamoyl)phenyl]propanoyl}-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (Y0Z)
Ligand formula: C43 H48 N10 O17 P2
Ligand molecular weight: 1038.846
Ligand SMILES: Cc1cc2c(cc1C)N(C3=C(N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O)NC(=O)NC3=O)C(=O)CCc7cccc(c7)C(=O)Nc8ccccc8
Ligand InChI: InChI=1S/C43H48N10O17P2/c1-21-13-26-27(14-22(21)2)53(31(56)12-11-23-7-6-8-24(15-23)40(60)48-25-9-4-3-5-10-25)33-39(49-43(62)50-41(33)61)51(26)16-28(54)34(57)29(55)17-67-71(63,64)70-72(65,66)68-18-30-35(58)36(59)42(69-30)52-20-47-32-37(44)45-19-46-38(32)52/h3-10,13-15,19-20,28-30,34-36,42,54-55,57-59H,11-12,16-18H2,1-2H3,(H,48,60)(H,63,64)(H,65,66)(H2,44,45,46)(H2,49,50,61,62)/t28-,29+,30+,34-,35+,36+,42+/m0/s1
Release date: 2024-06-26
Crystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound 7a (PDB entry 5NR8)
Macromolecule: Chitotriosidase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.14
Sequence length: 377 residues
Sequence: AKLVCYFTNWAQYRQGEARFLPKDLDPSLCTHLIYAFAGMTNHQLSTTEWNDETLYQEFNGLKKMNPKLKTLLAIGGWNFGTQKFTDMVATANNRQTFVNSAIRFLRKYSFDGLDLDWEYPGSQGSPAVDKERFTTLVQDLANAFQQEAQTSGKERLLLSAAVPAGQTYVDAGYEVDKIAQNLDFVNLMAYDFHGSWEKVTGHNSPLYKRQEESGAAASLNVDAAVQQWLQKGTPASKLILGMPTYGRSFTLASSSDTRVGAPATGSGTPGPFTKEGGMLAYYEVCSWKGATKQRIQDQKVPYIFRDNQWVGFDDVESFKTKVSYLKQKGLGGAMVWALDLDDFAGFSCNQGRYPLIQTLRQELSLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.349
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 25% (w/v) polyethylene glycol (PEG) 3350, 200 mM potassium sodium tartrate (PST) at pH 7.2
Matthews coefficient: 2.27
Solvent content (%): 45.88
Ligand: 1-(3-azanyl-1~{H}-1,2,4-triazol-5-yl)-~{N}-[2-(4-bromophenyl)ethyl]-~{N}-methyl-piperidin-4-amine (95N)
Ligand formula: C16 H23 Br N6
Ligand molecular weight: 379.298
Ligand SMILES: CN(CCc1ccc(cc1)Br)C2CCN(CC2)c3[nH]nc(n3)N
Ligand InChI: InChI=1S/C16H23BrN6/c1-22(9-6-12-2-4-13(17)5-3-12)14-7-10-23(11-8-14)16-19-15(18)20-21-16/h2-5,14H,6-11H2,1H3,(H3,18,19,20,21)
Release date: 2018-02-21
Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, N-oxalyl-alpha-methylalanine, and factor X substrate peptide fragment(39mer-4Ser) (PDB entry 6Z6R)
Macromolecule: Aspartyl/asparaginyl beta-hydroxylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.16
Sequence length: 429 residues
Sequence: KPKLLNKFDKTIKAELDAAEKLRKRGKIEEAVNAFKELVRKYPQSPRARYGKAQCEDDLAEKRRSNEVLRGAIETYQEVASLPDVPADLLKLSLKRRSDRQQFLGHMRGSLLTLQRLVQLFPNDTSLKNDLGVGYLLIGDNDNAKKVYEEVLSVTPNDGFAKVHYGFILKAQNKIAESIPYLKEGIESGDPGTDDGRFYFHLGDAMQRVGNKEAYKWYELGHKRGHFASVWQRSLYNVNGLKAQPWWTPKETGYTELVKSLERNWKLIRDEGLAVMDKAKGLFLPEDENLREKGDWSQFTLWQQGRRNENACKGAPKTCTLLEKFPETTGCRRGQIKYSIMHPGTHVWPHTGPTNCRLRMHLGLVIPKEGCKIRCANETKTWEEGKVLIFDDSFEHEVWQDASSFRLIFIVDVWHPELTPQQRRSLPAI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.2116
R free: 0.2424
Average B factor: 45.62
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Bis Tris propane, 200 mM sodium bromide, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM N-oxalyl-alpha-methylalanine, 18 mg/ml protein
Matthews coefficient: 2.67
Solvent content (%): 53.97
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: 2021-03-17
Crystal structure of human butyrylcholinesterase in complex with N-((1-benzylpiperidin-3-yl)methyl)-N-methylnaphthalene-2-sulfonamide (PDB entry 5DYT)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 530 residues
Sequence: TEDDIIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNPNETQNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.1789
R free: 0.2324
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M ammonium acetate, 12% polyethylene glycol 4000.
Matthews coefficient: 2.97
Solvent content (%): 58.55
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: 2016-10-05
Carbonic Anhydrase IX-mimic IN Complex WITH U-NO2 (PDB entry 5JMZ)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1615
R free: 0.1952
Average B factor: 21.6614
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M Na-Citrate, 50 mM Tris, pH 7.8
Matthews coefficient: 2.11
Solvent content (%): 41.75
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: 2017-05-03
Structure of CHK1 10-pt. mutant complex with pyrrolopyrimidine LRRK2 inhibitor (PDB entry 5OP5)
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): 1.9
R work: 0.1599
R free: 0.2057
Average B factor: 38.87
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol
Matthews coefficient: 2.31
Solvent content (%): 46.7
Ligand: 3-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile (3FE)
Ligand formula: C17 H15 N5 O
Ligand molecular weight: 305.334
Ligand SMILES: c1cc(cc(c1)c2c[nH]c3c2c(ncn3)N4CCOCC4)C#N
Ligand InChI: InChI=1S/C17H15N5O/c18-9-12-2-1-3-13(8-12)14-10-19-16-15(14)17(21-11-20-16)22-4-6-23-7-5-22/h1-3,8,10-11H,4-7H2,(H,19,20,21)
Release date: 2017-10-25
Cryogenic Human Hsp90a-NTD bound to BIIB021 (PDB entry 7S9F)
Macromolecule: Heat shock protein HSP 90-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.10
Sequence length: 237 residues
Sequence: HMPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFVEKERDKEVSDDEAE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2158
R free: 0.2461
Average B factor: 48.62
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 1.8 M Malic acid, pH 7
Matthews coefficient: 2.89
Solvent content (%): 57.37
Ligand: 6-chloro-9-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-9H-purin-2-amine (94M)
Ligand formula: C14 H15 Cl N6 O
Ligand molecular weight: 318.762
Ligand SMILES: Cc1cnc(c(c1OC)C)Cn2cnc3c2nc(nc3Cl)N
Ligand InChI: InChI=1S/C14H15ClN6O/c1-7-4-17-9(8(2)11(7)22-3)5-21-6-18-10-12(15)19-14(16)20-13(10)21/h4,6H,5H2,1-3H3,(H2,16,19,20)
Release date: 2022-08-03
Structure of Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSIR2rp1) in complex with acetylated p53 peptide (PDB entry 5OL0)
Macromolecule: Putative silent information regulator 2,Putative silent information regulator 2
Type: Protein, polypeptide(L)
Source organism: Leishmania infantum
EC number: 2.4.2.31
Sequence length: 324 residues
Sequence: GHMTASPRAPHQEHVLGEPTLEGLAHYIREKNVRRILVLVGAGASVAAGIPDFRSPDTGIYANLGKYNLEDPTDAFSLTLLREKPEIFYSIARELNLWPGHFQPTAVHHFIRLLQDEGRLLRCCTQNIDGLEKAAGVSPELLVEAHGSFAAAACIECHTPFSIEQNYLEAMSGTVSRCSTCGGIVKPNVVFFGENLPDAFFDALHHDAPIAELVIIIGTSMQVHPFALLPCVVPKSVPRVVMNRERVGGLLFRFASTSSSSDGYGQYGDYHAHPDVCRDVLFRGDCQENVVTLAEYLGLSEALAKRMRLSDAAPATAQRAPNET
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.16713
R free: 0.22577
Average B factor: 41.374
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 100mM Na Hepes pH7.5; 25% PEG2000 MME
Matthews coefficient: 2.06
Solvent content (%): 40.24
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
Binary complex crystal structure of DNA polymerase Beta with G:A mismatch at the primer terminus (PDB entry 5J0T)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2014
R free: 0.2581
Average B factor: 26.0252
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
Matthews coefficient: 2.4
Solvent content (%): 48.85
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2016-10-26
Human Carbonic Anhydrase II in complex with an inhibitor soaked at a concentration of 5 mM (PDB entry 6SDH)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 265 residues
Sequence: GSPEFMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.04
R work: 0.1311
R free: 0.1475
Average B factor: 14.88
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium sulfate 2.7 M, TRIS 0.1 M, saturated with para-Chloromercuribenzoic acid
Matthews coefficient: 2.08
Solvent content (%): 40.89
Ligand: N-[(2E)-3,4-dihydroquinazolin-2(1H)-ylidene]sulfuric diamide (0VV)
Ligand formula: C8 H10 N4 O2 S
Ligand molecular weight: 226.256
Ligand SMILES: c1ccc2c(c1)CNC(=NS(=O)(=O)N)N2
Ligand InChI: InChI=1S/C8H10N4O2S/c9-15(13,14)12-8-10-5-6-3-1-2-4-7(6)11-8/h1-4H,5H2,(H2,9,13,14)(H2,10,11,12)
Release date: 2020-08-26