satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of human plasma kallikrein protease domain with inhibitor (PDB entry 6O1S)
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): 1.7
R work: 0.1699
R free: 0.201
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 24% PEG 3350, 0.2M potassium dihydrogen phosphate
Matthews coefficient: 2.34
Solvent content (%): 47.51
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2019-03-06
ATAD2 bromodomain complexed with histone H4K5ac (res 1-10) ligand (PDB entry 7M98)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 152 residues
Sequence: GPLGSEPRSLTAEEVKRLEEQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLAEEIQESRKKRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.194
R free: 0.2187
Average B factor: 39.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2.0 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 6.6
Matthews coefficient: 3.05
Solvent content (%): 59.66
Release date: 2021-09-22
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000209a (PDB entry 7GT1)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.19
R free: 0.2225
Average B factor: 42.504
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.39
Solvent content (%): 63.72
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
The crystal structure of uPA in complex with HMA-55F (PDB entry 6AG7)
Macromolecule: Urokinase-type plasminogen activator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 245 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.19769
R free: 0.22847
Average B factor: 35.086
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 50 mM sodium citrate, pH 4.6, and 2.0 M ammonium sulfate supplemented with 5% polyethylene glycol 400
Matthews coefficient: 2.18
Solvent content (%): 43.66
Ligand: 3,5-diamino-N-carbamimidoyl-6-(1-methyl-1H-pyrazol-4-yl)pyrazine-2-carboxamide (H55)
Ligand formula: C10 H13 N9 O
Ligand molecular weight: 275.27
Ligand SMILES: Cn1cc(cn1)c2c(nc(c(n2)C(=O)NC(=N)N)N)N
Ligand InChI: InChI=1S/C10H13N9O/c1-19-3-4(2-15-19)5-7(11)17-8(12)6(16-5)9(20)18-10(13)14/h2-3H,1H3,(H4,11,12,17)(H4,13,14,18,20)
Release date: 2019-08-14
ERK2 covalently bound to SynthRevD-12-opt artificial peptide (PDB entry 8PSR)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 364 residues
Sequence: GSASMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1817
R free: 0.2091
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Na-citrate  pH 5.5, 20% PEG 8000
Matthews coefficient: 2.96
Solvent content (%): 58.4
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: 2024-07-24
structure of PTP-MEG2 and MUNC18-1-pY145 peptide complex (PDB entry 6L03)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 307 residues
Sequence: SVHVPGPHAMTIQELVDYVNARQKQGIYEEYEDIRRENPVGTFHCSMSPGNLEKNRYGDVPCLDQTRVKLTKRSGHTQTDYINASFMDGYKQKNAYIGTQGPLENTYRDFWLMVWEQKVLVIVMTTRFEEGGRRKCGQYWPLEKDSRIRFGFLTVTNLGVENMNHYKKTTLEIHNTEERQKRQVTHFQFLSWPAYGVPSSAASLIDFLRVVRNQQSLAVSNMGARSKGQCPEPPIVVHASAGIGRTGTFCSLDICLAQLEELGTLNVFQTVSRMRTQRAFSIQTPEQYYFCYKAILEFAEKEGMVSS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.084
R work: 0.2102
R free: 0.2304
Average B factor: 35.7581
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 4000, 0.2M KSCN, 10% ethelene glycol, 0.1M bis-tris propane
Matthews coefficient: 2.08
Solvent content (%): 40.76
Release date: 2020-09-30
human Artemis/SNM1C catalytic domain, crystal form 2 (PDB entry 6WNL)
Macromolecule: Protein artemis
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 375 residues
Sequence: SSFEGQMAEYPTISIDRFDRENLRARAYFLSHCHKDHMKGLRAPTLKRRLECSLKVYLYCSPVTKELLLTSPKYRFWKKRIISIEIETPTQISLVDEASGEKEEIVVTLLPAGHCPGSVMFLFQGNNGTVLYTGDFRLAQGEAARMELLHSGGRVKDIQSVYLDTTFCDPRFYQIPSREECLSGVLELVRSWITRSPYHVVWLNCKAAYGYEYLFTNLSEELGVQVHVNKLDMFRNMPEILHHLTTDRNTQIHACRHPKAEEYFQWSKLPCGITSRNRIPLHIISIKPSTMWFGERSRKTNVIVRTGESSYRACFSFHSSYSEIKDFLSYLCPVNAYPNVIPVGTTMDKVVEILKPLCRSSQSTEPKKGENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.37
R work: 0.2207
R free: 0.2803
Average B factor: 31.687
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 300
Crystal growth procedure: 50 mM MES pH 6.5, 0.1 M LiCl, 0.01 M MgCl2, 12% PEG 4000 (w/v)
Matthews coefficient: 2.45
Solvent content (%): 49.8
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-07-01
Crystal structure of HLA-A*11:01 in complex with KRAS G12D peptide (VVVGADGVGK) (PDB entry 7OW4)
Macromolecule: MHC class I antigen
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 276 residues
Sequence: GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.21968
R free: 0.24917
Average B factor: 26.136
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Lithium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3500
Matthews coefficient: 2.54
Solvent content (%): 51.63
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: 2022-07-20
Crystal structure of an effector in complex with ubiquitin (PDB entry 8HTF)
Macromolecule: NAD(+)--protein-threonine ADP-ribosyltransferase
Type: Protein, polypeptide(L)
Source organism: Chromobacterium violaceum ATCC 12472
EC number: 2.4.2
Sequence length: 233 residues
Sequence: SNRQEKLAQLMRQFESGGLYLRTVSDHRDEFENTFMPKLDACLGHGCDERYWSSATFIQQGLNGKVHDPHADRTGLIISADARLGGFSTFDAATANVPSGLEPSQYFPGQFPKFDMMGAYQATWNEDIFSVDATAVSEQQMDELGIPDEYRSVFDFDRIQEKMAQPRLAGREVEPTEAKICYQPKDVLGIYVDVDSPASQSKARELQQAMREQGFDLPFIAYRGGAAQELASV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.151
R work: 0.1726
R free: 0.2234
Average B factor: 39.117
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.25
Crystallization temperature (K): 289
Crystal growth procedure: 100 mM sodium cacodylate, pH 6.25, 200 mM sodium acetate, 22% PEG 8000, 25% glycerol
Matthews coefficient: 2.08
Solvent content (%): 40.81
Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NAD)
Ligand formula: C21 H27 N7 O14 P2
Ligand molecular weight: 663.425
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2023-11-22
Human APE1 substrate complex with an T/T mismatch adjacent the THF (PDB entry 6BOW)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 318 residues
Sequence: MPKRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.214
R free: 0.241
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Matthews coefficient: 2.3
Solvent content (%): 46.5
Release date: 2018-08-15
Crystal structure of PPARgamma with compound BR101549 (PDB entry 6ILQ)
Macromolecule: Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 272 residues
Sequence: PESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.408
R work: 0.2157
R free: 0.3035
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M MgCl2, 0.1 M TRIS 8.5 pH, 27 %w/v PEG 3350
Matthews coefficient: 2.07
Solvent content (%): 40.63
Ligand: ethyl [2-butyl-6-oxo-1-{[2'-(5-oxo-4,5-dihydro-1,2,4-oxadiazol-3-yl)[1,1'-biphenyl]-4-yl]methyl}-4-(propan-2-yl)-1,6-dihydropyrimidin-5-yl]acetate (AE0)
Ligand formula: C30 H34 N4 O5
Ligand molecular weight: 530.615
Ligand SMILES: CCCCC1=NC(=C(C(=O)N1Cc2ccc(cc2)c3ccccc3C4=NOC(=O)N4)CC(=O)OCC)C(C)C
Ligand InChI: InChI=1S/C30H34N4O5/c1-5-7-12-25-31-27(19(3)4)24(17-26(35)38-6-2)29(36)34(25)18-20-13-15-21(16-14-20)22-10-8-9-11-23(22)28-32-30(37)39-33-28/h8-11,13-16,19H,5-7,12,17-18H2,1-4H3,(H,32,33,37)
Release date: 2019-09-11
Tsetse thrombin inhibitor in complex with human alpha-thrombin - tetragonal form at 12.7keV (PDB entry 6TKI)
Macromolecule: Thrombin heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 259 residues
Sequence: IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1812
R free: 0.2143
Average B factor: 48.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.05 M sodium cacodylate pH 6.5, 0.01 M magnesium sulfate, 2 M ammonium sulfate
Matthews coefficient: 2.92
Solvent content (%): 57.9
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: 2020-11-04
Crystal structure of human chitotriosidase-1 catalytic domain in complex with chitobiose (0.3mM) at 1.10 A resolution (PDB entry 4WK9)
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): 1.102
R work: 0.1393
R free: 0.1537
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 25 % (w/v) polyethylene glycol (PEG) 3350, 0.2 M potassium sodium tartrate at pH 7.2, 0.3mM 4-methylumbelliferyl triacetylchitotrioside
Matthews coefficient: 2.23
Solvent content (%): 44.88
Release date: 2015-07-08
Crystal structure of bovine DNMT1 BAH1 domain in complex with H4K20me2 (PDB entry 7LMM)
Macromolecule: DNA (cytosine-5)-methyltransferase 1,DNA (cytosine-5)-methyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Bos taurus
EC number: 2.1.1.37
Sequence length: 158 residues
Sequence: SKNRISWVGDAVKTDGKKSYYKKVCIDSETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVQVIYKAPSGAGSATYFYQLWYDQDYARFESPPKTQPTEDNKYKFCASCARLA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.798
R work: 0.2066
R free: 0.2668
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M MES (pH 6.5) ,13% PEG1500, 20 mM DTT and 200 mM L-proline
Matthews coefficient: 2.45
Solvent content (%): 49.73
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: 2021-02-17
The crystal structure of human abl1 kinase domain in complex with ABL1-A11 (PDB entry 7W7X)
Macromolecule: Tyrosine-protein kinase ABL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 272 residues
Sequence: SPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQES
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.00000937681
R work: 0.168323023125
R free: 0.194598028559
Average B factor: 38.8330415441
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.0 M (NH4)2SO4 and 0.1 M HEPES (pH 7.0).
Matthews coefficient: 3.1
Solvent content (%): 60.38
Ligand: 5-[5-(dimethylcarbamoyl)pyridin-3-yl]-3-(5-fluorosulfonyloxy-2-methoxy-phenyl)-1H-pyrrolo[2,3-b]pyridine (8DW)
Ligand formula: C22 H19 F N4 O5 S
Ligand molecular weight: 470.473
Ligand SMILES: CN(C)C(=O)c1cc(cnc1)c2cc3c(c[nH]c3nc2)c4cc(ccc4OC)OS(=O)(=O)F
Ligand InChI: InChI=1S/C22H19FN4O5S/c1-27(2)22(28)15-6-13(9-24-10-15)14-7-18-19(12-26-21(18)25-11-14)17-8-16(32-33(23,29)30)4-5-20(17)31-3/h4-12H,1-3H3,(H,25,26)
Release date: 2022-04-27
Thrombin-RNA aptamer complex (PDB entry 5DO4)
Macromolecule: Thrombin light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.859
R work: 0.189
R free: 0.2236
Average B factor: 34.446
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 5% [w/v] PEG-6000, 2.5% v/v (+/-)-2-Methyl-2,4-pentanediol, 50 mM HEPES
Matthews coefficient: 3.14
Solvent content (%): 60.86
Ligand: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide (0G6)
Ligand formula: C21 H34 Cl N6 O3
Ligand molecular weight: 453.986
Ligand SMILES: c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NC(CCCNC(=[NH2+])N)C(CCl)O)N
Ligand InChI: InChI=1S/C21H33ClN6O3/c22-13-18(29)16(8-4-10-26-21(24)25)27-19(30)17-9-5-11-28(17)20(31)15(23)12-14-6-2-1-3-7-14/h1-3,6-7,15-18,29H,4-5,8-13,23H2,(H,27,30)(H4,24,25,26)/p+1/t15-,16+,17+,18-/m1/s1
Release date: 2016-09-14
HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 2F (PDB entry 7JIS)
Macromolecule: Phosphatidylinositol 3-kinase regulatory subunit alpha
Type: Protein, polypeptide(L)
Source organism: Bos taurus
Sequence length: 169 residues
Sequence: YQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEDYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNETEIQRIMHNYEKLKSRISEIVDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.42
R work: 0.2206
R free: 0.2671
Average B factor: 77.666
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG6000, 0.10 M KCL, 0.10 M MES pH 6.0
Matthews coefficient: 2.62
Solvent content (%): 53.09
Ligand: (3S)-3-benzyl-5-[9-ethyl-8-(2-methylpyrimidin-5-yl)-9H-purin-6-yl]-3-methyl-1,3-dihydro-2H-indol-2-one (VBS)
Ligand formula: C28 H25 N7 O
Ligand molecular weight: 475.544
Ligand SMILES: CCn1c2c(c(ncn2)c3ccc4c(c3)C(C(=O)N4)(C)Cc5ccccc5)nc1c6cnc(nc6)C
Ligand InChI: InChI=1S/C28H25N7O/c1-4-35-25(20-14-29-17(2)30-15-20)34-24-23(31-16-32-26(24)35)19-10-11-22-21(12-19)28(3,27(36)33-22)13-18-8-6-5-7-9-18/h5-12,14-16H,4,13H2,1-3H3,(H,33,36)/t28-/m0/s1
Release date: 2020-12-30
JAK2 JH2 in complex with JAK249 (PDB entry 7SZW)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.90646266564
R work: 0.192806573713
R free: 0.225748378017
Average B factor: 21.2111497036
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1M TRIS, PH 8.0 0.2M SODIUM ACETATE, 0.001 M TCEP, 12-24% PEG 4,000
Matthews coefficient: 2.32
Solvent content (%): 47
Ligand: 4-(4-{[5-amino-3-(4-sulfamoylanilino)-1H-1,2,4-triazole-1-carbonyl]amino}phenyl)pyridine-2-carboxylic acid (DVY)
Ligand formula: C21 H18 N8 O5 S
Ligand molecular weight: 494.483
Ligand SMILES: c1cc(ccc1c2ccnc(c2)C(=O)O)NC(=O)n3c(nc(n3)Nc4ccc(cc4)S(=O)(=O)N)N
Ligand InChI: InChI=1S/C21H18N8O5S/c22-19-27-20(25-14-5-7-16(8-6-14)35(23,33)34)28-29(19)21(32)26-15-3-1-12(2-4-15)13-9-10-24-17(11-13)18(30)31/h1-11H,(H,26,32)(H,30,31)(H2,23,33,34)(H3,22,25,27,28)
Release date: 2024-09-04
CHK1 KINASE IN COMPLEX WITH COMPOUND 44 (PDB entry 6FCF)
Macromolecule: Serine/threonine-protein kinase Chk1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 276 residues
Sequence: MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICINKMLNHENVVKFYGHRREGNIQYLFLEYCSGGELFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPENLLLDERDNLKISDFGLATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.2
R free: 0.232
Average B factor: 19.64
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 16% Peg8k, 0.1M Caco pH 6.8, 0.15M AS
Matthews coefficient: 2.56
Solvent content (%): 51.93
Ligand: 4-[[(2~{R},3~{S})-2-methylpiperidin-3-yl]amino]-2-phenyl-thieno[3,2-c]pyridine-7-carboxamide (D58)
Ligand formula: C20 H22 N4 O S
Ligand molecular weight: 366.48
Ligand SMILES: CC1C(CCCN1)Nc2c3cc(sc3c(cn2)C(=O)N)c4ccccc4
Ligand InChI: InChI=1S/C20H22N4OS/c1-12-16(8-5-9-22-12)24-20-14-10-17(13-6-3-2-4-7-13)26-18(14)15(11-23-20)19(21)25/h2-4,6-7,10-12,16,22H,5,8-9H2,1H3,(H2,21,25)(H,23,24)/t12-,16+/m1/s1
Release date: 2018-01-17
Human Carbonic Anhydrase II in complex with 4-Ethylbenzenesulfonamide (PDB entry 6HQX)
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): 1.097
R work: 0.1218
R free: 0.1389
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium sulfate 2.70 M, pH = 7.8, saturated with p-Chloromercuribenzoic acid
Matthews coefficient: 2.06
Solvent content (%): 40.18
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: 2019-10-09