satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of HER2 Domain IV and Rb-H2 (PDB entry 6LBX)
Macromolecule: Repebody (Rb-H2)
Type: Protein, polypeptide(L)
Source organism: Cyclostomata
Sequence length: 275 residues
Sequence: METITVSTPIKQIFPDDAFAETIKANLKKKSVTDAVTQNELNSIDLISAPHSDIKSVQGIQYLPNVRLLYLGGNKLHDISALKELTNLTTLILSGNQLQSLPNGVFDKLTNLKVLWLSVNQLQSLPDGVFDKLTNLTSLRLHRNQLQSLPKGVFDKLTNLTVLRLSENQLQSLPEGVFDKLTQLKVLWLGRNQLKSVPDGVFDRLTSLQYIWLHDNPWDCTCPGIRYLSEWINKHSGVVRNSAGSVAPDSAKCSGSGKPVRSIICPTLEHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.1902
R free: 0.2277
Average B factor: 31.98
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 290
Crystal growth procedure: 0.1M Sodium Citrate/Citric Acid (pH 5.5), 20% PEG 3000
Matthews coefficient: 2.33
Solvent content (%): 47.25
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: 2020-11-18
PI4K IIalpha bound to calcium (PDB entry 5I0N)
Macromolecule: Phosphatidylinositol 4-kinase type 2-alpha,Lysozyme,Phosphatidylinositol 4-kinase type 2-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.67
Sequence length: 556 residues
Sequence: GAMGTVAAQAQALAAQAAAAAHAAQAHRERNEFPEDPEFEAVVRQAELAIERCIFPERIYQGSSGSYFVKDPQGRIIAVFKPKNEEPYGHLNPKWTKWLQKGTGNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNLGRDCLVLNQGYLSEAGASLVDQKLELNIVPRTKVVYLASETFNYSAIDRVKSRGKRLALEKVPKVGQRFNRIGLPPKVGSFQLFVEGYKDADYWLRRFEAEPLPENTNRQLLLQFERLVVLDYIIRNTDRGNDNWLIKYDCPMDSSSSRDTDWVVVKEPVIKVAAIDNGLAFPLKHPDSWRAYPFYWAWLPQAKVPFSQEIKDLILPKISDPNFVKDLEEDLYELFKKDPGFDRGQFHKQIAVMRGQILNLTQALKDNKSPLHLVQMPPVIVETARSHQRSSSESYTQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.2192
R free: 0.2577
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1 M bicine/Trizma base pH 8.5
Matthews coefficient: 2.51
Solvent content (%): 51.02
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: 2016-03-09
human carbonic anhydrase II in complex with ligand (PDB entry 5EH5)
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): 1.207
R work: 0.171
R free: 0.1867
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 280
Crystal growth procedure: ammonium sulfate, tris-chloride
Matthews coefficient: 2.06
Solvent content (%): 40.19
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: 2016-03-09
LSD1-CoREST-S2101 five-membered ring adduct model (PDB entry 6KGK)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 669 residues
Sequence: GPLGSHMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1772
R free: 0.2064
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.23 M potassium sodium tartrate
Matthews coefficient: 6.93
Solvent content (%): 82.25
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: 2020-03-25
MerTK kinase domain in complex with purine inhibitor (PDB entry 7AW0)
Macromolecule: Tyrosine-protein kinase Mer
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 298 residues
Sequence: GSHMEELQNKLEDVVIDRNLLILGRILGEGEFGSVMEGNLKQEDGTSLKVAVKTMKLDNSSQREIEEFLSEAACMKDFSHPNVIRLLGVCIEMSSQGIPKPMVILPFMKYGDLHTYLLYSRLETGPRHIPLQTLLRFMVDIALGMEYLSNRNFLHRDLAARNCMLRDDMTVCVADFGLSKKIYSGDYYRQGRIAKMPVKWIAIESLADRVYTSKSDVWAFGVTMWEIATRGMTPYPGVQNHEMYDYLLHGHRLKQPEDCLDELYEIMYSCWRTDPLDRPTFSVLRLQLERLLESLPDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.893
R work: 0.202
R free: 0.233
Average B factor: 51.53
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 4.0-4.5 M sodium chloride, 0.1 M Tris pH 8.5: 16 h soak with 20 % DMSO and 20 mM compound
Matthews coefficient: 2.23
Solvent content (%): 44.96
Ligand: 2-(cyclopentyloxy)-9-(2,6-difluorobenzyl)-N-methyl-9H-purin-6-amine (S4Q)
Ligand formula: C18 H19 F2 N5 O
Ligand molecular weight: 359.373
Ligand SMILES: CNc1c2c(nc(n1)OC3CCCC3)n(cn2)Cc4c(cccc4F)F
Ligand InChI: InChI=1S/C18H19F2N5O/c1-21-16-15-17(24-18(23-16)26-11-5-2-3-6-11)25(10-22-15)9-12-13(19)7-4-8-14(12)20/h4,7-8,10-11H,2-3,5-6,9H2,1H3,(H,21,23,24)
Release date: 2021-03-03
Crystal structure of human GPX4-U46C in complex with MAC-5576 (PDB entry 7U4L)
Macromolecule: Phospholipid hydroperoxide glutathione peroxidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.1.12
Sequence length: 192 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMLEAASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQCGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1634
R free: 0.2299
Average B factor: 34.2225
Crystallization method: MICROBATCH
Crystallization pH: 4.6
Crystallization temperature (K): 291
Crystal growth procedure: 2 M sodium chloride and 0.1 M sodium acetate trihydrate
Matthews coefficient: 2.3
Solvent content (%): 46.45
Ligand: thiophene-2-carbaldehyde (LW1)
Ligand formula: C5 H4 O S
Ligand molecular weight: 112.15
Ligand SMILES: c1cc(sc1)C=O
Ligand InChI: InChI=1S/C5H4OS/c6-4-5-2-1-3-7-5/h1-4H
Release date: 2022-12-07
Crystal Structure of KDM4A with Compound 14 (PDB entry 6CG1)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 350 residues
Sequence: SETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.16
R work: 0.1749
R free: 0.2403
Average B factor: 40.985
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG4K, 150mM NaCl, 50mMHEPES pH 7.3
Matthews coefficient: 2.52
Solvent content (%): 51.19
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2018-04-18
ERK2 mini-fragment binding (PDB entry 6QAQ)
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): 1.58
R work: 0.188
R free: 0.229
Average B factor: 30.095
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M (NH4)2SO4
34% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.28
Solvent content (%): 46.04
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: 2019-03-27
Carbonic Anhydrase II in complex with 4-ureido benzenesulfonamide derivative (PDB entry 7RNZ)
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): 1.3
R work: 0.1582
R free: 0.1836
Average B factor: 15.6086
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M sodium citrate, 50 mM tris base
Matthews coefficient: 2.09
Solvent content (%): 41.12
Ligand: 4-[(methylcarbamoyl)amino]benzene-1-sulfonamide (64W)
Ligand formula: C8 H11 N3 O3 S
Ligand molecular weight: 229.256
Ligand SMILES: CNC(=O)Nc1ccc(cc1)S(=O)(=O)N
Ligand InChI: InChI=1S/C8H11N3O3S/c1-10-8(12)11-6-2-4-7(5-3-6)15(9,13)14/h2-5H,1H3,(H2,9,13,14)(H2,10,11,12)
Release date: 2022-06-08
The Fk1 domain of FKBP51 in complex with 2-(3-((1R)-1-(((2S)-1-(2-cyclohexyl-2-(thiophen-2-yl)acetyl)piperidine-2-carbonyl)oxy)-3-(3,4-dimethoxyphenyl)propyl)phenoxy)acetic acid (PDB entry 8CCH)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.2098
R free: 0.2349
Average B factor: 33.938
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 26% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate, 10% ethylene glycol
Matthews coefficient: 2.77
Solvent content (%): 55.52
Ligand: 2-[3-[(1~{R})-1-[(2~{S})-1-[(2~{S})-2-cyclohexyl-2-thiophen-2-yl-ethanoyl]piperidin-2-yl]carbonyloxy-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid (U8C)
Ligand formula: C37 H45 N O8 S
Ligand molecular weight: 663.82
Ligand SMILES: COc1ccc(cc1OC)CCC(c2cccc(c2)OCC(=O)O)OC(=O)C3CCCCN3C(=O)C(c4cccs4)C5CCCCC5
Ligand InChI: InChI=1S/C37H45NO8S/c1-43-31-19-17-25(22-32(31)44-2)16-18-30(27-12-8-13-28(23-27)45-24-34(39)40)46-37(42)29-14-6-7-20-38(29)36(41)35(33-15-9-21-47-33)26-10-4-3-5-11-26/h8-9,12-13,15,17,19,21-23,26,29-30,35H,3-7,10-11,14,16,18,20,24H2,1-2H3,(H,39,40)/t29-,30+,35+/m0/s1
Release date: 2023-04-26
Crystal structure of human HBO1 in complex with BRPF2 (PDB entry 5GK9)
Macromolecule: Histone acetyltransferase KAT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 276 residues
Sequence: MIKTIAFGRYELDTWYHSPYPEEYARLGRLYMCEFCLKYMKSQTILRRHMAKCVWKHPPGDEIYRKGSISVFEVDGKKNKIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVMTEADNTGCHLIGYFSKEKNSFLNYNVSCILTMPQYMRQGYGKMLIDFSYLLSKVEEKVGSPERPLSDLGLISYRSYWKEVLLRYLHNFQGKEISIKEISQETAVNPVDIVSTLQALQMLKYWKGKHLVLKRQDLIDEWIAKEAKRSNSNKTMDPSCLKWTPPKGT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.233
R free: 0.26
Average B factor: 49.289
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: Tacsimate Tris-HCl, PEG 3350
Matthews coefficient: 2.41
Solvent content (%): 48.98
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: 2017-03-29
VDR complex with Aromatic-D-Ring Analog (PDB entry 7ZFX)
Macromolecule: Vitamin D3 receptor A
Type: Protein, polypeptide(L)
Source organism: Danio rerio
Sequence length: 302 residues
Sequence: GSHMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNHSPESVDTKLNFSNLLMMYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEVS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.208
R free: 0.2538
Average B factor: 67.1394
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: NaActetae 2.5M, Tris 0.1M
Matthews coefficient: 2.33
Solvent content (%): 47.1
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2022-11-23
Aurora A in complex with ATP and AA35. (PDB entry 5DN3)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 272 residues
Sequence: GSMGSKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1915
R free: 0.203
Average B factor: 45.62
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 292
Crystal growth procedure: 50 mM HEPES, 200 mM magnesium sulfate, 20% PEG 3350
Matthews coefficient: 3.62
Solvent content (%): 66
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: 2016-07-20
Bruton's tyrosine kinase in complex with compound 1 (PDB entry 6W07)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 293 residues
Sequence: GPLGSRLKYPVSQQNKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51
R work: 0.2292
R free: 0.2671
Average B factor: 15.44
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: bis-tris, ammonium salt, PEG
Matthews coefficient: 2.08
Solvent content (%): 40.93
Ligand: ~{N}-[[2-methyl-4-[2-[(1-methylpyrazol-4-yl)amino]pyrimidin-4-yl]phenyl]methyl]-3-propan-2-yloxy-azetidine-1-carboxamide (S9A)
Ligand formula: C23 H29 N7 O2
Ligand molecular weight: 435.522
Ligand SMILES: Cc1cc(ccc1CNC(=O)N2CC(C2)OC(C)C)c3ccnc(n3)Nc4cnn(c4)C
Ligand InChI: InChI=1S/C23H29N7O2/c1-15(2)32-20-13-30(14-20)23(31)25-10-18-6-5-17(9-16(18)3)21-7-8-24-22(28-21)27-19-11-26-29(4)12-19/h5-9,11-12,15,20H,10,13-14H2,1-4H3,(H,25,31)(H,24,27,28)
Release date: 2020-12-16
Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with 5-((2-(4H-1,2,4-triazol-4-yl)pyridin-4-yl)amino)-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidine-3-carbonitrile (PDB entry 8P06)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 338 residues
Sequence: SMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.20158
R free: 0.23728
Average B factor: 58.84
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350
Matthews coefficient: 3.16
Solvent content (%): 61.09
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: 2023-06-21
FACTOR XIA IN COMPLEX WITH THE INHIBITOR METHYL ((12E,15S)-15-(((2E)-3-(5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL)-2-PROPENOYL)AMINO)-9-OXO-8,17,19-TRIAZATRICYCLO[14.2.1.0~2,7~]NONADECA-1(18),2,4,6,12,16(19)-HEXAEN-5-YL)CARBAMATE (PDB entry 5TKT)
Macromolecule: Factor XIa (Light Chain)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.1667
R free: 0.1888
Average B factor: 24.87
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 100 MM SODIUM ACETATE, PH 4.6, 25%(w/v) MEPEG2000, 200 MM AMMONIUM SULFATE, then transferred to 100 MM TRIS-HCL, pH 7.0, 25%(w/v) MEPEG2000, 200 MM AMMONIUM SULFATE
Matthews coefficient: 3.43
Solvent content (%): 64.18
Ligand: METHYL
((12E,15S)-15-(((2E)-3-(5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL)-2-PROPENOYL)AMINO)-9-OXO-8,17,19-TRIAZATRICYCLO[14.2.1.0~2,
7~]NONADECA-1(18),2,4,6,12,16(19)-HEXAEN-5-YL)CARBAMATE (7DS)
Ligand formula: C28 H26 Cl N9 O4
Ligand molecular weight: 588.017
Ligand SMILES: COC(=O)Nc1ccc-2c(c1)NC(=O)CCC=CCC(c3[nH]cc2n3)NC(=O)C=Cc4cc(ccc4n5cnnn5)Cl
Ligand InChI: InChI=1S/C28H26ClN9O4/c1-42-28(41)32-19-9-10-20-22(14-19)34-25(39)6-4-2-3-5-21(27-30-15-23(20)35-27)33-26(40)12-7-17-13-18(29)8-11-24(17)38-16-31-36-37-38/h2-3,7-16,21H,4-6H2,1H3,(H,30,35)(H,32,41)(H,33,40)(H,34,39)/b3-2+,12-7+/t21-/m0/s1
Release date: 2017-03-01
Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 80 s (PDB entry 5VS0)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 341 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2019
R free: 0.2621
Average B factor: 32.588
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
Matthews coefficient: 2.23
Solvent content (%): 44.95
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: 2017-07-19
Crystal structure of HDAC8 in complex with compound 30 (PDB entry 6ODC)
Macromolecule: Histone deacetylase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 413 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNAMEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVIEGRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.1944
R free: 0.23577
Average B factor: 76.315
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.3
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MES pH5.3, 5% PEG6000, 0.14 M Gly-Gly-Gly, 2mM TCEP
Matthews coefficient: 2.67
Solvent content (%): 53.96
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2020-04-01
Crystal structure of PTK6 Kinase domain with inhibitor (PDB entry 5DA3)
Macromolecule: Protein-tyrosine kinase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 265 residues
Sequence: MERPREEFTLCRKLGSGYFGEVFEGLWKDRVQVAIKVISRDNLLHQQMLQSEIQAMKKLRHKHILALYAVVSVGDPVYIITELMAKGSLLELLRDSDEKVLPVSELLDIAWQVAEGMCYLESQNYIHRDLAARNILVGENTLCKVGDFGLARLIKEDVYLSHDHNIPYKWTAPEALSRGHYSTKSDVWSFGILLHEMFSRGQVPYPGMSNHEAFLRVDAGYRMPCPLECPPSVHKLMLTCWCRDPEQRPTFKALRERLSSFTSHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1974
R free: 0.2302
Average B factor: 22.476
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 0.2 M tri-Lithium citrate, 20% (w/v) PEG 3350
Matthews coefficient: 2.48
Solvent content (%): 50.45
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: 2016-08-24