satarupa22/MacromolecularLigandDB huggingface dataset:
LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N67 i.e. 2-(5-phenyl-4-(phenyl(2-(piperidin-1-yl)ethoxy)methyl)-1H-pyrazol-1-yl)isonicotinic acid (PDB entry 6DQE)
Macromolecule: Linked KDM5A Jmj Domain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.689
R work: 0.1748
R free: 0.1873
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.22
Solvent content (%): 44.66
Ligand: 2-(5-phenyl-4-{(R)-phenyl[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrazol-1-yl)pyridine-4-carboxylic acid (H6A)
Ligand formula: C29 H30 N4 O3
Ligand molecular weight: 482.574
Ligand SMILES: c1ccc(cc1)c2c(cnn2c3cc(ccn3)C(=O)O)C(c4ccccc4)OCCN5CCCCC5
Ligand InChI: InChI=1S/C29H30N4O3/c34-29(35)24-14-15-30-26(20-24)33-27(22-10-4-1-5-11-22)25(21-31-33)28(23-12-6-2-7-13-23)36-19-18-32-16-8-3-9-17-32/h1-2,4-7,10-15,20-21,28H,3,8-9,16-19H2,(H,34,35)/t28-/m1/s1
Release date: 2019-06-12
Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with a pyrazolo[3,4-d]pyrimidine fragment of NVP-BHG712 (PDB entry 6FNK)
Macromolecule: Ephrin type-B receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 297 residues
Sequence: GMDPNEAVREFAKEIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTLKGGYTERQRREFLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLNDGQFTVIQLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDFGLSRFLEENSSDPTETSSLGGKIPIRWTAPEAIAFRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDYRLPPPPDCPTSLHQLMLDCWQKDRNARPRFPQIVSALDKMIRNPASLKIVARENG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.049
R work: 0.1983
R free: 0.2202
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 10 % PEG5000 MME, 0.15 M MgCl2, 15 % Glycerol, 0.1 M TRIS pH 7.5
Matthews coefficient: 2.03
Solvent content (%): 39.6
Ligand: 1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-amine (DXK)
Ligand formula: C11 H10 N6
Ligand molecular weight: 226.237
Ligand SMILES: Cn1c2c(cn1)c(nc(n2)c3cccnc3)N
Ligand InChI: InChI=1S/C11H10N6/c1-17-11-8(6-14-17)9(12)15-10(16-11)7-3-2-4-13-5-7/h2-6H,1H3,(H2,12,15,16)
Release date: 2018-08-08
Structure of Ku80 von Willebrand domain complexed with WRN Ku Binding Motif (PDB entry 6TYV)
Macromolecule: X-ray repair cross-complementing protein 5
Type: Protein, polypeptide(L)
Source organism: Xenopus laevis
EC number: 3.6.4
Sequence length: 231 residues
Sequence: MHHHHHHMARAAKSAVVLCMDVGLAMSHSNQGKESPFEQAKKVMMLFLQRQVFAESKDEIAVVLYGTDTTDNALAREDQYENISVHRHLMLPDFDLLEQIENVVEPGSVQADFLDALIVSMDLLQKETLGKKYTRLHIAVFSDLSSPFSVDQLEVIIANLKKAEITLQFFLPFSVDEGSGPGKGLSDQQKEGIEMVRKIMFSLDGEEGLSEVFTFRDSLERLSIFKKIERR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92611100742
R work: 0.192609532857
R free: 0.234844595656
Average B factor: 46.2047717462
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M Na-HEPES pH 7.5, 25 % (w/v) PEG3000
Matthews coefficient: 2.09
Solvent content (%): 41.19
Release date: 2019-11-27
Crystal structure of BACE complex with BMC025 (PDB entry 5QCQ)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 402 residues
Sequence: GPDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.167
R free: 0.195
Average B factor: 39.15
Crystallization method: hanging drop
Crystallization temperature (K): 292
Crystal growth procedure: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM SULFATE IN WATER. PROTEIN STOCK WAS
BACE MUT46B BATCH XII 8.5MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 5-FOLD EXCESS OF BMC025 ADDED FROM A 50MM
STOCK SOLUTION IN 90% DMSO-D6 (1.8% DMSO IN DROP). A SOLUTION CONTAINING 1.2M AMMONIUM SULFATE, 25% GLYCEROL, 1MM BMC025
AND 1.8% DMSO WAS USED AS CRYO-PROTECTANT.
Matthews coefficient: 3.1
Solvent content (%): 60.26
Ligand: (2R,4S,5S)-N-butyl-4-hydroxy-2,7-dimethyl-5-{[N-(4-methylpentanoyl)-L-methionyl]amino}octanamide (AFJ)
Ligand formula: C25 H49 N3 O4 S
Ligand molecular weight: 487.739
Ligand SMILES: CCCCNC(=O)C(C)CC(C(CC(C)C)NC(=O)C(CCSC)NC(=O)CCC(C)C)O
Ligand InChI: InChI=1S/C25H49N3O4S/c1-8-9-13-26-24(31)19(6)16-22(29)21(15-18(4)5)28-25(32)20(12-14-33-7)27-23(30)11-10-17(2)3/h17-22,29H,8-16H2,1-7H3,(H,26,31)(H,27,30)(H,28,32)/t19-,20+,21+,22+/m1/s1
Release date: 2020-06-03
Crystal structure of the MZM-REP domains of Mind bomb 1 in complex with Jagged1 N-box peptide (PDB entry 4XI7)
Macromolecule: E3 ubiquitin-protein ligase MIB1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 380 residues
Sequence: SRVMVEGVGARVVRGPDWKWGKQDGGEGHVGTVRSFESPEEVVVVWDNGTAANYRCSGAYDLRILDSAPTGIKHDGTMCDTCRQQPIIGIRWKCAECTNYDLCTVCYHGDKHHLRHRFYRITTPGSERVLLESRRKSKKITARGIFAGARVVRGVDWQWEDQDGGNGRRGKVTEIQDWSASSPHSAAYVLWDNGAKNLYRVGFEGMSDLKCVQDAKGGSFYRDHCPVLGEQNGNRNPGGLQIGDLVNIDLDLEIVQSLQHGHGGWTDGMFETLTTTGTVCGIDEDHDIVVQYPSGNRWTFNPAVLTKASQFQVGDLVQVCYDLERIKLLQRGHGEWAEAMLPTLGKVGRVQQIYSDSDLKVEVCGTSWTYNPAAVSKVAS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.051
R work: 0.1967
R free: 0.2236
Average B factor: 44.892
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: Protein at 6 mg/mL in 25 mM HEPES 7.4, 500 mM NaCl, 10% w/v glucose, 100 mM Arg, 2 mM TCEP
Precipitant: 1.5 M (NH4)2SO4, 20% v/v glycerol, HEPES pH 7.6
1:1 drop volume
Matthews coefficient: 2.66
Solvent content (%): 53.77
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: 2015-03-18
Discovery of new selenoureido analogs of 4-(4-fluorophenylureido) benzenesulfonamides as carbonic anhydrase inhibitors (PDB entry 5WEX)
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): 1.26
R work: 0.11785
R free: 0.14655
Average B factor: 16.971
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 281
Crystal growth procedure: concentrated CA II at about 10 mg/mL was set up in SD-2 plates with the following ratio of protein plus reservoir plus seeds: 250nL plus 225 nL plus 25 nL. The plate was incubated at 8C and the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.
3
Matthews coefficient: 2.11
Solvent content (%): 41.67
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: 2017-10-11
Crystal structure of JAK2 JH2-V617F in complex with JNJ-7706621 (PDB entry 8B99)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCFCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAWAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1891
R free: 0.2108
Average B factor: 35.41
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Tris pH 8, 22% PEG4000, 0.2M Na-acetate
Matthews coefficient: 2.61
Solvent content (%): 52.8
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: 2023-02-01
Bovine GRK2 in complex with Gbetagamma subunits and CCG224406 (PDB entry 5HE2)
Macromolecule: Beta-adrenergic receptor kinase 1
Type: Protein, polypeptide(L)
Source organism: Bos taurus
EC number: 2.7.11.15
Sequence length: 641 residues
Sequence: KKILLPEPSIRSVMQKYLEDRGEVTFEKIFSQKLGYLLFRDFCLKHLEEAKPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIMKELLACSHPFSKSAIEHVQGHLVKKQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFCQWKNVELNIHLTMNDFSVHRIIGRGGFGEVYGCRKADTGKMYAMKCLDKKRIKMKQGETLALNERIMLSLVSTGDCPFIVCMSYAFHTPDKLSFILDLMNGGDLHYHLSQHGVFSEADMRFYAAEIILGLEHMHNRFVVYRDLKPANILLDEHGHVRISDLGLACDFSKKKPHASVGTHGYMAPEVLQKGVAYDSSADWFSLGCMLFKLLRGHSPFRQHKTKDKHEIDRMTLTMAVELPDSFSPELRSLLEGLLQRDVNRRLGCLGRGAQEVKESPFFRSLDWQMVFLQKYPPPLIPPRGEVNAADAFDIGSFDEEDTKGIKLLDSDQELYRNFPLTISERWQQEVAETVFDTINAETDRLEARKKTKNKQLGHEEDYALGKDCIMHGYMSKMGNPFLTQWQRRYFYLFPNRLEWRGEGEAPQSLLTMEEIQSVEETQIKERKCLLLKIRGGKQFVLQCDSDPELVQWKKELRDAYREAQQLVQRVPKMKNKPRA
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.79
R work: 0.1981
R free: 0.2773
Average B factor: 70.769
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 50 mM MES, 0.8-1.2 M sodium chloride, 8-16% PEG3350
Matthews coefficient: 3.42
Solvent content (%): 64.03
Ligand: (4~{S})-4-[3-[(2,6-dimethoxyphenyl)methylcarbamoyl]-4-fluoranyl-phenyl]-~{N}-(1~{H}-indazol-5-yl)-6-methyl-2-oxidanylidene-3,4-dihydro-1~{H}-pyrimidine-5-carboxamide (F0S)
Ligand formula: C29 H27 F N6 O5
Ligand molecular weight: 558.56
Ligand SMILES: CC1=C(C(NC(=O)N1)c2ccc(c(c2)C(=O)NCc3c(cccc3OC)OC)F)C(=O)Nc4ccc5c(c4)cn[nH]5
Ligand InChI: InChI=1S/C29H27FN6O5/c1-15-25(28(38)34-18-8-10-22-17(11-18)13-32-36-22)26(35-29(39)33-15)16-7-9-21(30)19(12-16)27(37)31-14-20-23(40-2)5-4-6-24(20)41-3/h4-13,26H,14H2,1-3H3,(H,31,37)(H,32,36)(H,34,38)(H2,33,35,39)/t26-/m0/s1
Release date: 2016-05-11
Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives (PDB entry 5LSX)
Macromolecule: Histone-lysine N-methyltransferase SETD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 295 residues
Sequence: MHHHHHHSSGRENLYFQGETSVPPGSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKKNKSHRDIKRMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGKMKKERSRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.17947
R free: 0.28025
Average B factor: 122.365
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Hepes, pH 7.3, 0.1MKSCN, 25-30%MPEG2000
Matthews coefficient: 2.2
Solvent content (%): 44.1
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: 2016-10-05
The Crystal Structure of N-terminal kinase domain of human RSK-1 from Biortus. (PDB entry 8XOV)
Macromolecule: Ribosomal protein S6 kinase alpha-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 321 residues
Sequence: QPSKDEGVLKEISITHHVKAGSEKADPSHFELLKVLGQGSFGKVFLVRKVTRPDSGHLYAMKVLKKATLKVRDRVRTKMERDILADVNHPFVVKLHYAFQTEGKLYLILDFLRGGDLFTRLSKEVMFTEEDVKFYLAELALGLDHLHSLGIIYRDLKPENILLDEEGHIKLTDFGLSKEAIDHEKKAYSFCGTVEYMAPEVVNRQGHSHSADWWSYGVLMFEMLTGSLPFQGKDRKETMTLILKAKLGMPQFLSTEAQSLLRALFKRNPANRLGSGPDGAEEIKRHVFYSTIDWNKLYRREIKPPFKPAVAQPDDTFYFDT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.2032
R free: 0.2517
Average B factor: 64.192
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MgAC2, 0.1M Nacacodylate pH6.5, 15% PEG 6000
Matthews coefficient: 2.89
Solvent content (%): 57.49
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2024-03-06
Lemur tyrosine kinase 3 (LMTK3) (PDB entry 6SEQ)
Macromolecule: Serine/threonine-protein kinase LMTK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 1460 residues
Sequence: MPAPGALILLAAVSASGCLASPAHPDGFALGRAPLAPPYAVVLISCSGLLAFIFLLLTCLCCKRGDVGFKEFENPEGEDCSGEYTPPAEETSSSQSLPDVYILPLAEVSLPMPAPQPSHSDMTTPLGLSRQHLSYLQEIGSGWFGKVILGEIFSDYTPAQVVVKELRASAGPLEQRKFISEAQPYRSLQHPNVLQCLGLCVETLPFLLIMEFCQLGDLKRYLRAQRPPEGLSPELPPRDLRTLQRMGLEIARGLAHLHSHNYVHSDLALRNCLLTSDLTVRIGDYGLAHSNYKEDYYLTPERLWIPLRWAAPELLGELHGTFMVVDQSRESNIWSLGVTLWELFEFGAQPYRHLSDEEVLAFVVRQQHVKLARPRLKLPYADYWYDILQSCWRPPAQRPSASDLQLQLTYLLSERPPRPPPPPPPPRDGPFPWPWPPAHSAPRPGTLSSPFPLLDGFPGADPDDVLTVTESSRGLNLECLWEKARRGAGRGGGAPAWQPASAPPAPHANPSNPFYEALSTPSVLPVISARSPSVSSEYYIRLEEHGSPPEPLFPNDWDPLDPGVPAPQAPQAPSEVPQLVSETWASPLFPAPRPFPAQSSASGSFLLSGWDPEGRGAGETLAGDPAEVLGERGTAPWVEEEEEEEEGSSPGEDSSSLGGGPSRRGPLPCPLCSREGACSCLPLERGDAVAGWGGHPALGCPHPPEDDSSLRAERGSLADLPMAPPASAPPEFLDPLMGAAAPQYPGRGPPPAPPPPPPPPRAPADPAASPDPPSAVASPGSGLSSPGPKPGDSGYETETPFSPEGAFPGGGAAEEEGVPRPRAPPEPPDPGAPRPPPDPGPLPLPGPREKPTFVVQVSTEQLLMSLREDVTRNLLGEKGATARETGPRKAGRGPGNREKVPGLNRDPTVLGNGKQAPSLSLPVNGVTVLENGDQRAPGIEEKAAENGALGSPEREEKVLENGELTPPRREEKALENGELRSPEAGEKVLVNGGLTPPKSEDKVSENGGLRFPRNTERPPETGPWRAPGPWEKTPESWGPAPTIGEPAPETSLERAPAPSAVVSSRNGGETAPGPLGPAPKNGTLEPGTERRAPETGGAPRAPGAGRLDLGSGGRAPVGTGTAPGGGPGSGVDAKAGWVDNTRPQPPPPPLPPPPEAQPRRLEPAPPRARPEVAPEGEPGAPDSRAGGDTALSGDGDPPKPERKGPEMPRLFLDLGPPQGNSEQIKARLSRLSLALPPLTLTPFPGPGPRRPPWEGADAGAAGGEAGGAGAPGPAEEDGEDEDEDEEEDEEAAAPGAAAGPRGPGRARAAPVPVVVSSADADAARPLRGLLKSPRGADEPEDSELERKRKMVSFHGDVTVYLFDQETPTNELSVQAPPEGDTDPSTPPAPPTPPHPATPGDGFPSNDSGFGGSFEWAEDFPLLPPPGPPLCFSRFSVSPALETPGPPARAPDARPAGPVEN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.194
R free: 0.262
Average B factor: 25.01
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: LMTK3 at 3.2 mg/ml in 20 mM Tris pH 7.5, 200 mM NaCl was crystallised with 70 mM bis-Tris Propane pH 6.5, 14 % w/v Polyethylene Glycol 3350, 14 mM Sodium/Potassium Phosphate, 30 % w/v sucrose
Matthews coefficient: 3.05
Solvent content (%): 59.63
Release date: 2020-11-25
Matriptase in complex with the synthetic inhibitor (S)-3-(3-(4-(3-(tert-butyl)ureido)piperidin-1-yl)-2-((3'-fluoro-4'-(hydroxymethyl)-[1,1'-biphenyl])-3-sulfonamido)-3-oxopropyl)benzimidamide (MI-1904) (PDB entry 6T9T)
Macromolecule: Suppressor of tumorigenicity 14 protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.109
Sequence length: 241 residues
Sequence: VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGFRYSDPTQWTAFLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIALLELEKPAEYSSMVRPISLPDASHVFPAGKAIWVTGWGHTQYGGTGALILQKGEIRVINQTTCENLLPQQITPRMMCVGFLSGGVDSCQGDSGGPLSSVEADGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTGV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.170323632146
R free: 0.201903857021
Average B factor: 25.5897796376
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM Sodium acetate pH 4.6, 2 M Sodium formate, protein concentration 7 mg/ml
Matthews coefficient: 2.37
Solvent content (%): 48.05
Ligand: 1-~{tert}-butyl-3-[1-[(2~{S})-3-(3-carbamimidoylphenyl)-2-[[3-[3-fluoranyl-4-(hydroxymethyl)phenyl]phenyl]sulfonylamino
]propanoyl]piperidin-4-yl]urea (MXH)
Ligand formula: C33 H41 F N6 O5 S
Ligand molecular weight: 652.779
Ligand SMILES: CC(C)(C)NC(=O)NC1CCN(CC1)C(=O)C(Cc2cccc(c2)C(=N)N)NS(=O)(=O)c3cccc(c3)c4ccc(c(c4)F)CO
Ligand InChI: InChI=1S/C33H41FN6O5S/c1-33(2,3)38-32(43)37-26-12-14-40(15-13-26)31(42)29(17-21-6-4-8-24(16-21)30(35)36)39-46(44,45)27-9-5-7-22(18-27)23-10-11-25(20-41)28(34)19-23/h4-11,16,18-19,26,29,39,41H,12-15,17,20H2,1-3H3,(H3,35,36)(H2,37,38,43)/t29-/m0/s1
Release date: 2020-11-18
Crystal Structure of KRAS-G12V (GMPPNP-bound) in complex with RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF (PDB entry 6XHA)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.87
R work: 0.2167
R free: 0.2691
Average B factor: 102.9443
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM sodium cacodylate pH 6.5, 200 mM MgCl2, 8% PGA, 0.35 mM D-myo-phosphatidylinositol 3,4,5-triphosphate
Matthews coefficient: 3.23
Solvent content (%): 61.96
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2021-01-13
Crystal structure of the BRAF:MEK1 kinases in complex with AMPPNP and PD0325901 (PDB entry 7M0X)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 283 residues
Sequence: GGGRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.47
R work: 0.1781
R free: 0.2151
Average B factor: 48.58
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Bis-Tris pH 6.4, 200 mM Ammonium Sulfate, and 22% PEG3350
Matthews coefficient: 3.38
Solvent content (%): 63.56
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2021-04-21
Room-temperature Human Hsp90a-NTD bound to EC144 (PDB entry 7S9I)
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): 1.75
R work: 0.1665
R free: 0.1914
Average B factor: 45.9
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 1.8 M Malic acid, pH 7
Matthews coefficient: 2.9
Solvent content (%): 57.57
Ligand: 5-{2-amino-4-chloro-7-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-7H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-methylpent-4-yn-2
-ol (7PP)
Ligand formula: C21 H24 Cl N5 O2
Ligand molecular weight: 413.901
Ligand SMILES: Cc1cnc(c(c1OC)C)Cn2cc(c3c2nc(nc3Cl)N)C#CCC(C)(C)O
Ligand InChI: InChI=1S/C21H24ClN5O2/c1-12-9-24-15(13(2)17(12)29-5)11-27-10-14(7-6-8-21(3,4)28)16-18(22)25-20(23)26-19(16)27/h9-10,28H,8,11H2,1-5H3,(H2,23,25,26)
Release date: 2022-08-03
Structure of recombinant human butyrylcholinesterase in complex with a fluorescent NBD-based probe (PDB entry 6R6W)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 526 residues
Sequence: IIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.474
R work: 0.1822
R free: 0.2268
Average B factor: 66.7131
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate
Matthews coefficient: 3.2
Solvent content (%): 61.59
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: 2020-01-15