satarupa22/MacromolecularLigandDB huggingface dataset:
CDK2 in complex with FragLite16 (PDB entry 6Q4C)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 306 residues
Sequence: GPLGSPEFMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.17999
R free: 0.22267
Average B factor: 28.759
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 10MG/ML CDK2 10% V/V PEG3350, 50 MM HEPES/NAOH, 50 MM NA/K PHOSPHATE, PH 7.5
Matthews coefficient: 1.96
Solvent content (%): 37.24
Ligand: 4-bromanyl-1,8-naphthyridine (HH8)
Ligand formula: C8 H5 Br N2
Ligand molecular weight: 209.043
Ligand SMILES: c1cc2c(ccnc2nc1)Br
Ligand InChI: InChI=1S/C8H5BrN2/c9-7-3-5-11-8-6(7)2-1-4-10-8/h1-5H
Release date: 2019-03-20
Structure of human plasma kallikrein (PDB entry 5TJX)
Macromolecule: Plasma kallikrein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.34
Sequence length: 263 residues
Sequence: NTGDNSVCTTKTSTRIVGGTESSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILELSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLEYTEFQKPISLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSDGKAQMQSPA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.408
R work: 0.1626
R free: 0.1842
Average B factor: 19.3
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 0.2 M potassium di-hydrogen phosphate, 21 % PEG 3350
Matthews coefficient: 2.17
Solvent content (%): 43.42
Ligand: (8E)-3-amino-1-methyl-15-[(1H-pyrazol-1-yl)methyl]-7,10,11,12,24,25-hexahydro-6H,18H,23H-19,22-(metheno)pyrido[4,3-j][1,9,13,17,18]benzodioxatriazacyclohenicosin-23-one (GBT)
Ligand formula: C29 H33 N7 O3
Ligand molecular weight: 527.617
Ligand SMILES: Cc1c2c(cc(n1)N)OCCC=CCCCOc3cc(ccc3Cn4cc(cn4)C(=O)NC2)Cn5cccn5
Ligand InChI: InChI=1S/C29H33N7O3/c1-21-25-17-31-29(37)24-16-33-36(20-24)19-23-9-8-22(18-35-11-7-10-32-35)14-26(23)38-12-5-3-2-4-6-13-39-27(25)15-28(30)34-21/h2,4,7-11,14-16,20H,3,5-6,12-13,17-19H2,1H3,(H2,30,34)(H,31,37)/b4-2+
Release date: 2016-12-21
Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA<sub>2</sub>) Discovered Through X-Ray Fragment Screening (PDB entry 5JAN)
Macromolecule: Platelet-activating factor acetylhydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.47
Sequence length: 388 residues
Sequence: MAAASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTTNQHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.22291
R free: 0.26693
Average B factor: 34.96
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 297
Crystal growth procedure: 1.0M NaCl, 0.1M HEPES/NaOHpH=7.4, 28.8%w/v PEG 3350
Matthews coefficient: 2.33
Solvent content (%): 47.2
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2016-05-25
Crystal structure of the active catalytic core of the human DEAD-box protein DDX3 bound to AMP (PDB entry 5E7J)
Macromolecule: ATP-dependent RNA helicase DDX3X
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 452 residues
Sequence: EDDWSKPLPPSERLEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYEHHYKGSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.2298
R free: 0.2637
Average B factor: 37.4013
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: PEG 3000, sodium citrate
Matthews coefficient: 2.43
Solvent content (%): 49.42
Ligand: ADENOSINE MONOPHOSPHATE (AMP)
Ligand formula: C10 H14 N5 O7 P
Ligand molecular weight: 347.221
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2015-12-02
Crystal Structure of human cyclic GMP-AMP synthase in complex with 6-(2-chloro-4-methylphenyl)-3-[3-(methanesulfonamido)propyl]benzimidazole-4-carboxylic acid (PDB entry 7FUL)
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): 2.296
R work: 0.1905
R free: 0.2732
Average B factor: 55.0316
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: 2.12
Solvent content (%): 41.96
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: 2024-02-21
Bromodomain of Human GCN5 with 4-bromo-2-methyl-5-(((3R,5R)-1-methyl-5-phenylpiperidin-3-yl)amino)pyridazin-3(2H)-one (PDB entry 5MLJ)
Macromolecule: Histone acetyltransferase KAT2A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 112 residues
Sequence: SMEDPDQLYTTLKNLLAQIKSHPSAWPFMEPVKKSEAPDYYEVIRFPIDLKTMTERLRSRYYVTRKLFVADLQRVIANCREYNPPDSEYCRCASALEKFFYFKLKEGGLIDK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.16669
R free: 0.21101
Average B factor: 17.319
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M Ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350
Matthews coefficient: 2.55
Solvent content (%): 51.7
Ligand: 4-bromo-2-methyl-5-[[(3~{R},5~{R})-1-methyl-5-phenyl-piperidin-3-yl]amino]pyridazin-3-one (9ST)
Ligand formula: C17 H21 Br N4 O
Ligand molecular weight: 377.279
Ligand SMILES: CN1CC(CC(C1)NC2=C(C(=O)N(N=C2)C)Br)c3ccccc3
Ligand InChI: InChI=1S/C17H21BrN4O/c1-21-10-13(12-6-4-3-5-7-12)8-14(11-21)20-15-9-19-22(2)17(23)16(15)18/h3-7,9,13-14,20H,8,10-11H2,1-2H3/t13-,14+/m0/s1
Release date: 2017-12-20
PLK-1 polo-box domain in complex with a high affinity macrocycle synthesized using a novel glutamic acid analog (PDB entry 7MX1)
Macromolecule: Serine/threonine-protein kinase PLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.21
Sequence length: 237 residues
Sequence: GAHMDCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSRSASNRLKAS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.1754
R free: 0.2041
Average B factor: 45.6897
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M. CaCl2, 15% PEG-3350
Matthews coefficient: 2.36
Solvent content (%): 47.84
Ligand: N-[(4S)-4,5-diamino-5-oxopentyl]-10-phenyldecanamide (ZOY)
Ligand formula: C21 H35 N3 O2
Ligand molecular weight: 361.522
Ligand SMILES: c1ccc(cc1)CCCCCCCCCC(=O)NCCCC(C(=O)N)N
Ligand InChI: InChI=1S/C21H35N3O2/c22-19(21(23)26)15-11-17-24-20(25)16-10-5-3-1-2-4-7-12-18-13-8-6-9-14-18/h6,8-9,13-14,19H,1-5,7,10-12,15-17,22H2,(H2,23,26)(H,24,25)/t19-/m0/s1
Release date: 2022-03-30
Crystal structure of human MTH1(G2K mutant) in complex with 8-oxo-dGTP at pH 9.1 (PDB entry 8I1C)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 156 residues
Sequence: MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1525
R free: 0.1844
Average B factor: 17.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: sodium citrate, caps, NaCl
Matthews coefficient: 1.88
Solvent content (%): 34.62
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2023-03-22
Human Cyclophilin D in complex with N-(4-aminophenyl)-7-methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide (PDB entry 7R2L)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MGNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.134
R free: 0.1533
Average B factor: 14.36
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277.15
Crystal growth procedure: 15 % PEG 3350, 0.1M K2HPO4
Matthews coefficient: 2.01
Solvent content (%): 38.88
Ligand: N-(4-aminophenyl)-7-methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide (UX5)
Ligand formula: C15 H15 N5 O2
Ligand molecular weight: 297.312
Ligand SMILES: CC1=C(C=NC2=CC(=O)NN12)C(=O)NCc3ccc(cc3)N
Ligand InChI: InChI=1S/C15H15N5O2/c1-9-12(8-17-13-6-14(21)19-20(9)13)15(22)18-7-10-2-4-11(16)5-3-10/h2-6,8H,7,16H2,1H3,(H,18,22)(H,19,21)
Release date: 2023-02-15
Crystal Structure of DYRK1A with small molecule inhibitor (PDB entry 6S1B)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 361 residues
Sequence: SMSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1606
R free: 0.1786
Average B factor: 21.3736
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2.2M ammonium sulfate -- 0.1M citrate pH 5.3 -- 0.2M sodium/potassium tartrate
Matthews coefficient: 2.74
Solvent content (%): 55.15
Ligand: ~{N}-methyl-4-pyrazolo[1,5-b]pyridazin-3-yl-pyrimidin-2-amine (KRQ)
Ligand formula: C11 H10 N6
Ligand molecular weight: 226.237
Ligand SMILES: CNc1nccc(n1)c2cnn3c2cccn3
Ligand InChI: InChI=1S/C11H10N6/c1-12-11-13-6-4-9(16-11)8-7-15-17-10(8)3-2-5-14-17/h2-7H,1H3,(H,12,13,16)
Release date: 2019-06-26
FGFR2 Kinase Domain Bound to Reversible Inhibitor Cmpd 3 (PDB entry 8SWE)
Macromolecule: Fibroblast growth factor receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 316 residues
Sequence: SHMGSPMLAGVSEYELPEDPKWEFPRDKLTLGKPLGEGCFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPGMEYSYDINRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKKTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLTTNEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.2112
R free: 0.2496
Average B factor: 46.73
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 27 % PEG 4000, 0.1 M Hepes pH7.5, 0.252 M Ammonium Sulfate, 0.05 M GSH GSSG
Matthews coefficient: 2.77
Solvent content (%): 55.64
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: 2024-02-14
CypA Mutant - I97V S99T C115S (PDB entry 5WC7)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGVLTMANAGPNTNGSQFFISTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1037
R free: 0.1273
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 100 MM HEPES PH 7.5, 22% PEG 3350
Matthews coefficient: 2.79
Solvent content (%): 55.91
Release date: 2018-04-18
PCSK9 in complex with a Fab and compound 8 (PDB entry 6U38)
Macromolecule: Proprotein convertase subtilisin/kexin type 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 707 residues
Sequence: QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQSIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAGWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRDVSTTGSTSEEAVTAVAICCRSRHLAQASQELQKGNSADIQHSGGRSSLEGPRFEGKPIPNPLLGLDSTRTGHHHHHH
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.73
R work: 0.227
R free: 0.243
Average B factor: 57.73
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Bicine pH9.0, 2% dioxane, 10% PEG 20000
Matthews coefficient: 2.61
Solvent content (%): 52.82
Ligand: 2-fluoro-4-{[(1R)-1-methyl-6-{[(2S)-oxan-2-yl]methoxy}-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}-1,2,3,4-tetrahydroisoquinolin-7-yl]oxy}benzoic acid (PVJ)
Ligand formula: C28 H30 F N3 O6 S
Ligand molecular weight: 555.618
Ligand SMILES: CC1(c2cc(c(cc2CCN1)OCC3CCCCO3)Oc4ccc(c(c4)F)C(=O)O)CC(=O)Nc5nccs5
Ligand InChI: InChI=1S/C28H30FN3O6S/c1-28(15-25(33)32-27-30-9-11-39-27)21-14-24(38-18-5-6-20(26(34)35)22(29)13-18)23(12-17(21)7-8-31-28)37-16-19-4-2-3-10-36-19/h5-6,9,11-14,19,31H,2-4,7-8,10,15-16H2,1H3,(H,34,35)(H,30,32,33)/t19-,28+/m0/s1
Release date: 2019-11-06
BIO-8546 bound GSK3beta-axin complex (PDB entry 7SXH)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 347 residues
Sequence: VTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHAR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.2138
R free: 0.2554
Average B factor: 57.64
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.2M calcium acetate, 0.1M BisTRIS pH 7.0, 5% Glycerol and 17% PEG3350
Matthews coefficient: 2.43
Solvent content (%): 49.46
Ligand: (4S,5R,8R)-4-ethyl-8-fluoro-4-[3-(3-fluoro-5-methoxypyridin-4-yl)phenyl]-7,7-dimethyl-4,5,6,7,8,9-hexahydro-2H-pyrazolo[3,4-b]quinolin-5-ol (D1E)
Ligand formula: C26 H28 F2 N4 O2
Ligand molecular weight: 466.523
Ligand SMILES: CCC1(c2c[nH]nc2NC3=C1C(CC(C3F)(C)C)O)c4cccc(c4)c5c(cncc5F)OC
Ligand InChI: InChI=1S/C26H28F2N4O2/c1-5-26(15-8-6-7-14(9-15)20-17(27)12-29-13-19(20)34-4)16-11-30-32-24(16)31-22-21(26)18(33)10-25(2,3)23(22)28/h6-9,11-13,18,23,33H,5,10H2,1-4H3,(H2,30,31,32)/t18-,23+,26+/m1/s1
Release date: 2023-06-14
Crystal structure of ERK2 in complex with an inhibitor 14K (PDB entry 4XJ0)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 349 residues
Sequence: EMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58
R work: 0.2084
R free: 0.2438
Average B factor: 82.76
Crystallization method: EVAPORATION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% PEG3350, 0.2 M proline, and 0.1 M HEPES pH7.5, in a 24-well Linbro plates
Matthews coefficient: 2.92
Solvent content (%): 57.94
Ligand: 1-[(1S)-1-(4-chloro-3-fluorophenyl)-2-hydroxyethyl]-4-[2-(tetrahydro-2H-pyran-4-ylamino)pyrimidin-4-yl]pyridin-2(1H)-one (41B)
Ligand formula: C22 H22 Cl F N4 O3
Ligand molecular weight: 444.886
Ligand SMILES: c1cc(c(cc1C(CO)N2C=CC(=CC2=O)c3ccnc(n3)NC4CCOCC4)F)Cl
Ligand InChI: InChI=1S/C22H22ClFN4O3/c23-17-2-1-15(11-18(17)24)20(13-29)28-8-4-14(12-21(28)30)19-3-7-25-22(27-19)26-16-5-9-31-10-6-16/h1-4,7-8,11-12,16,20,29H,5-6,9-10,13H2,(H,25,26,27)/t20-/m1/s1
Release date: 2015-09-16
Re-refinement of 6ESR human IBA57 at 1.75 A resolution (PDB entry 6QE3)
Macromolecule: Putative transferase CAF17, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1
Sequence length: 309 residues
Sequence: AGAAWACFRLDGRTLLRVRGPDAAPFLLGLLTNELPLPSPAAAGAPPAARAGYAHFLNVQGRTLYDVILYGLQEHSEVSGFLLECDSSVQGALQKHLALYRIRRKVTVEPHPELRVWAVLPSSPEACGAASLQERAGAAAILIRDPRTARMGWRLLTQDEGPALVPGGRLGDLWDYHQHRYLQGVPEGVRDLPPGVALPLESNLAFMNGVSFTKGCYIGQELTARTHHMGVIRKRLFPVRFLDPLPTSGITPGATVLTASGQTVGKFRAGQGNVGLALLWSEKIKGPLHIRASEGAQVALAASVPDWWP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1746
R free: 0.1971
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES, 20% PEG3350
Matthews coefficient: 2.53
Solvent content (%): 51.31
Release date: 2019-03-13
Crystal structure of ADP-riboxanated caspase-4 in complex with Af1521 (PDB entry 7WR6)
Macromolecule: Caspase-4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.57
Sequence length: 280 residues
Sequence: SGRPSTDALKLCPHEEFLRLCKERAEEIYPIKERNNRTRLALIICNTEFDHLPPRNGADFDITGMKELLEGLDYSVDVEENLTARDMESALRAFATRPEHKSSDSTFLVLMSHGILEGICGTVHDEKKPDVLLYDTIFQIFNNRNCLSLKDKPKVIIVQAARGANRGELWVRDSPASLEVASSQSSENLEEDAVYKTHVEKDFIAFCSSTPHNVSWRDSTMGSIFITQLITCFQKYSWCCHLEEVFRKVQQSFETPRAKAQMPTIERLSMTRYFYLFPGN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1962
R free: 0.2283
Average B factor: 43.7
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 27% PEG 3350, 0.05M CAPSO pH 9.0
Matthews coefficient: 2.17
Solvent content (%): 43.42
Ligand: [[(3~{a}~{S},5~{R},6~{R},6~{a}~{R})-2-azanylidene-3-[(4~{R})-4-azanyl-5-oxidanylidene-pentyl]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxazol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate (5ZY)
Ligand formula: C21 H32 N8 O14 P2
Ligand molecular weight: 682.472
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C5C(O4)N(C(=N)O5)CCCC(C=O)N)O)O)O)N
Ligand InChI: InChI=1S/C21H32N8O14P2/c22-9(4-30)2-1-3-28-20-16(42-21(28)24)14(32)11(41-20)6-39-45(36,37)43-44(34,35)38-5-10-13(31)15(33)19(40-10)29-8-27-12-17(23)25-7-26-18(12)29/h4,7-11,13-16,19-20,24,31-33H,1-3,5-6,22H2,(H,34,35)(H,36,37)(H2,23,25,26)/b24-21-/t9-,10-,11-,13-,14-,15-,16-,19-,20+/m1/s1
Release date: 2023-01-25
Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5) (PDB entry 6F4T)
Macromolecule: JmjC domain-containing protein 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.47
Sequence length: 255 residues
Sequence: HHHHHHSSGVDLGTENLYFQSTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPAMQKWSLEYIQEIAGARTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFCWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.22
R work: 0.1413
R free: 0.1544
Average B factor: 26
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M Bis-Tris pH 6.5, 17.1 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:1 ratio)
Matthews coefficient: 2.3
Solvent content (%): 46.64
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: 2018-04-04