satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311 (PDB entry 6VZH)
Macromolecule: Serine/threonine-protein kinase VRK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.2157
R free: 0.2514
Average B factor: 63.234
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 27.5% PEG3350, 300 mM lithium sulfate, 0.1 M sodium tartrate, 0.1 M Bis-Tris, 0.1 M glycylglycine, cryoprotectant: 30% glycerol
Matthews coefficient: 2.58
Solvent content (%): 52.31
Ligand: (7~{R})-2-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]amino]-5,7-dimethyl-8-prop-2-ynyl-7~{H}-pteridin-6-one (RYA)
Ligand formula: C17 H15 F2 N5 O2
Ligand molecular weight: 359.33
Ligand SMILES: CC1C(=O)N(c2cnc(nc2N1CC#C)Nc3cc(c(c(c3)F)O)F)C
Ligand InChI: InChI=1S/C17H15F2N5O2/c1-4-5-24-9(2)16(26)23(3)13-8-20-17(22-15(13)24)21-10-6-11(18)14(25)12(19)7-10/h1,6-9,25H,5H2,2-3H3,(H,20,21,22)/t9-/m1/s1
Release date: 2020-03-11
Crystal Structure of Mnk2-D228G in Complex With Inhibitor (PDB entry 6CJ5)
Macromolecule: MAP kinase-interacting serine/threonine-protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 316 residues
Sequence: GSTDSFSGRFEDVYQLQEDVLGEGAHARVQTCINLITSQEYAVKIIEKQPGHIRSRVFREVEMLYQCQGHRNVLELIEFFEEEDRFYLVFEKMRGGSILSHIHKRRHFNELEASVVVQDVASALDFLHNKGIAHRDLKPENILCEHPNQVSPVKICDFGLGSGIKLNGDCSPISTPELLTPCGSAEYMAPEVVEAFSEEASIYDKRCDLWSLGVILYILLSGYPPFVGRCGSDCGWDRGEACPACQNMLFESIQEGKYEFPDKDWAHISCAAKDLISKLLVRDAKQRLSAAQVLQHPWVQGCAPENTLPTPMVLQR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.20371
R free: 0.28002
Average B factor: 68.537
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 300.15
Crystal growth procedure: 20-30% (w/v) polyacrylic acid 5100, 1-5% PEG 400, and 50 mM Hepes (pH 7.5)
Matthews coefficient: 3.26
Solvent content (%): 62.26
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2018-05-09
Crystal Structure of double mutant Y115E Y117E human Glutaminyl Cyclase in complex with inhibitor PBD-150 (PDB entry 4YWY)
Macromolecule: Glutaminyl-peptide cyclotransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.5
Sequence length: 361 residues
Sequence: MAGGRHRRVVGTLHLLLLVAALPWASRGVSPSASAWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPEGERSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDSAVPCAMMLELARALDKKLLSLKTVSDSKPDLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.16408
R free: 0.21101
Average B factor: 13.098
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 281
Crystal growth procedure: 0.1 M MES buffer pH 6.5, 1.6 M ammonium sulfate
Matthews coefficient: 2.52
Solvent content (%): 51.16
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: 2015-08-05
Crystal structure of MTH1 in apo form (cocktail No. 1) (PDB entry 6AA3)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 163 residues
Sequence: MASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTVLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.001
R work: 0.2101
R free: 0.2571
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG3350, 1.8 mM ZnSO4, 6% sucrose, 0.1 M Bis-Tris pH 6.1
Matthews coefficient: 2.08
Solvent content (%): 40.93
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: 2019-03-06
Crystal structure of RIP1 kinase in complex with GSK3145095 (PDB entry 6RLN)
Macromolecule: Receptor-interacting serine/threonine-protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 303 residues
Sequence: MDYKDDDDKMQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLAFHRTQGLMIMKTVYKGPNCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELREVDGTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAIAEQQLIMAIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.87
R work: 0.1939
R free: 0.2318
Average B factor: 99.26
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 100mM MES (pH 6.5), 25% PEG 8k
Matthews coefficient: 2.35
Solvent content (%): 47.66
Ligand: ~{N}-[(3~{S})-7,9-bis(fluoranyl)-2-oxidanylidene-1,3,4,5-tetrahydro-1-benzazepin-3-yl]-3-(phenylmethyl)-1~{H}-1,2,4-triazole-5-carboxamide (K8K)
Ligand formula: C20 H17 F2 N5 O2
Ligand molecular weight: 397.378
Ligand SMILES: c1ccc(cc1)Cc2nc([nH]n2)C(=O)NC3CCc4cc(cc(c4NC3=O)F)F
Ligand InChI: InChI=1S/C20H17F2N5O2/c21-13-9-12-6-7-15(19(28)25-17(12)14(22)10-13)23-20(29)18-24-16(26-27-18)8-11-4-2-1-3-5-11/h1-5,9-10,15H,6-8H2,(H,23,29)(H,25,28)(H,24,26,27)/t15-/m0/s1
Release date: 2019-07-03
Specific covalent inhibitor (3) of ERK2 (PDB entry 8AO2)
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): 1.796
R work: 0.1698
R free: 0.2189
Average B factor: 25.183
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.25M (NH4)2SO4
33% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.29
Solvent content (%): 46.17
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: 2022-09-28
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster11 (PDB entry 7GU4)
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): 1.59
R work: 0.195
R free: 0.2239
Average B factor: 39.257
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: 3.31
Solvent content (%): 62.84
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: 2024-01-31
A fragment-based inhibitor of SHP2 (PDB entry 8RZY)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 537 residues
Sequence: HMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.17576
R free: 0.2201
Average B factor: 52.238
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.5M K formate
15% PEG 3350
0.1M pH=8 Bis-Tris propane/HCl
Matthews coefficient: 2.16
Solvent content (%): 43.15
Ligand: 1H-pyrrolo[3,2-b]pyridin-5-amine (A1H4L)
Ligand formula: C7 H7 N3
Ligand molecular weight: 133.151
Ligand SMILES: c1cc(nc2c1[nH]cc2)N
Ligand InChI: InChI=1S/C7H7N3/c8-7-2-1-5-6(10-7)3-4-9-5/h1-4,9H,(H2,8,10)
Release date: 2024-03-20
Novel Spiro[3H-indole-3,2 -pyrrolidin]-2(1H)-one Inhibitors of the MDM2-p53 Interaction: HDM2 (MDM2) IN COMPLEX WITH COMPOUND 14 (PDB entry 5LAW)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 94 residues
Sequence: QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.1929
R free: 0.2158
Average B factor: 12.93
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: RESERVOIR SOLUTION : NULL
Matthews coefficient: 2.27
Solvent content (%): 45.79
Ligand: 2-[(3~{S},3'~{a}~{S},6'~{S},6'~{a}~{S})-6-chloranyl-6'-(3-chlorophenyl)-4'-(cyclopropylmethyl)-2-oxidanylidene-spiro[1~{H}-indole-3,5'-3,3~{a},6,6~{a}-tetrahydro-2~{H}-pyrrolo[3,2-b]pyrrole]-1'-yl]ethanoic acid (6SJ)
Ligand formula: C25 H25 Cl2 N3 O3
Ligand molecular weight: 486.39
Ligand SMILES: c1cc(cc(c1)Cl)C2C3C(CCN3CC(=O)O)N(C24c5ccc(cc5NC4=O)Cl)CC6CC6
Ligand InChI: InChI=1S/C25H25Cl2N3O3/c26-16-3-1-2-15(10-16)22-23-20(8-9-29(23)13-21(31)32)30(12-14-4-5-14)25(22)18-7-6-17(27)11-19(18)28-24(25)33/h1-3,6-7,10-11,14,20,22-23H,4-5,8-9,12-13H2,(H,28,33)(H,31,32)/t20-,22-,23+,25+/m0/s1
Release date: 2016-11-02
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue (PDB entry 6CTR)
Macromolecule: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(2DA))-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 10 residues
Sequence: GCTGATGCGA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.172
R free: 0.222
Average B factor: 29.59
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.29
Solvent content (%): 46.36
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: 2018-06-20
Human Carbonic Anhydrase II in complex with (3-((N-(4-sulfamoylphenethyl)phenylsulfonamido)methyl)phenyl)glycine (PDB entry 8QF9)
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): 1.277
R work: 0.1299
R free: 0.1631
Average B factor: 12.063
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Matthews coefficient: 2.12
Solvent content (%): 41.89
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: 2024-09-11
Crystal structure of the Abl 1b Kinase domain in complex with Dasatinib and Imatinib (PDB entry 7N9G)
Macromolecule: Tyrosine-protein kinase ABL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 271 residues
Sequence: SPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2174
R free: 0.2511
Average B factor: 52.067
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: Ammonium dihydrogen phosphate
Matthews coefficient: 2.88
Solvent content (%): 57.36
Ligand: N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE (1N1)
Ligand formula: C22 H26 Cl N7 O2 S
Ligand molecular weight: 488.006
Ligand SMILES: Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cc(nc(n3)C)N4CCN(CC4)CCO)Cl
Ligand InChI: InChI=1S/C22H26ClN7O2S/c1-14-4-3-5-16(23)20(14)28-21(32)17-13-24-22(33-17)27-18-12-19(26-15(2)25-18)30-8-6-29(7-9-30)10-11-31/h3-5,12-13,31H,6-11H2,1-2H3,(H,28,32)(H,24,25,26,27)
Release date: 2022-04-27
Crystal structure of human ATAD2 bromodomain in complex with (2S)-2,6- diacetamido-N-methylhexanamide (PDB entry 5A5N)
Macromolecule: ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.18001
R free: 0.19596
Average B factor: 32.945
Crystal growth procedure: 50MM BIS-TRIS PROPANE, PH7, 300MM NACL, 1MM DTT, 10% GLYCEROL
Matthews coefficient: 4.03
Solvent content (%): 69.48
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: 2015-07-22
Crystal structure of JNK3 in complex with FMU-001-367 (compound 1) (PDB entry 7ORF)
Macromolecule: Mitogen-activated protein kinase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 365 residues
Sequence: SMSKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.167
R free: 0.2046
Average B factor: 25.265
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277.15
Crystal growth procedure: 34% PEG400 and 0.1 M MES, pH 6.0
Matthews coefficient: 2.5
Solvent content (%): 50.86
Ligand: N-[4-[[4-[5-(4-fluorophenyl)-3-methyl-2-methylsulfanyl-imidazol-4-yl]pyridin-2-yl]amino]phenyl]-3-(propanoylamino)benzamide (0G3)
Ligand formula: C32 H29 F N6 O2 S
Ligand molecular weight: 580.675
Ligand SMILES: CCC(=O)Nc1cccc(c1)C(=O)Nc2ccc(cc2)Nc3cc(ccn3)c4c(nc(n4C)SC)c5ccc(cc5)F
Ligand InChI: InChI=1S/C32H29FN6O2S/c1-4-28(40)36-26-7-5-6-22(18-26)31(41)37-25-14-12-24(13-15-25)35-27-19-21(16-17-34-27)30-29(38-32(42-3)39(30)2)20-8-10-23(33)11-9-20/h5-19H,4H2,1-3H3,(H,34,35)(H,36,40)(H,37,41)
Release date: 2021-07-21
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z31792168 (PDB entry 5QIF)
Macromolecule: Hydroxyacid oxidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.3.15
Sequence length: 369 residues
Sequence: SMLPRLICINDYEQHAKSVLPKSIYDYYRSGANDEETLADNIAAFSRWKLYPRMLRNVAETDLSTSVLGQRVSMPICVGATAMQRMAHVDGELATVRACQSLGTGMMLSSWATSSIEEVAEAGPEALRWLQLYIYKDREVTKKLVRQAEKMGYKAIFVTVDTPYLGNRLDDVRNRFKLPPQLRMKNFETSTLSFSPEENFGDDSGLAAYVAKAIDPSISWEDIKWLRRLTSLPIVAKGILRGDDAREAVKHGLNGILVSNHGARQLDGVPATIDVLPEIVEAVEGKVEVFLDGGVRKGTDVLKALALGAKAVFVGRPIVWGLAFQGEKGVQDVLEILKEEFRLAMALSGCQNVKVIDKTLVRKNPLAVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.163
R free: 0.1829
Average B factor: 14.218
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.75
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MIB pH 5.75 - 7.0, 27.5-35% PEG1000
Matthews coefficient: 2.38
Solvent content (%): 48.3
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2018-07-18
Crystal structure of human RIPK1 kinase domain in complex with compound RI-962 (PDB entry 7YDX)
Macromolecule: Receptor-interacting serine/threonine-protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 294 residues
Sequence: MQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLAFHRTQGLMIMKTVYKGPNCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELREVDGTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAIAEQQLIMAIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLE
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.642
R work: 0.2603
R free: 0.2892
Average B factor: 42.1556
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.25M ammonium iodide, 0.03M glycyl-glycyl-glycine, 23% polyethylene glycol (PEG) 3350
Matthews coefficient: 2.29
Solvent content (%): 46.38
Ligand: 1-methyl-5-[2-(2-methylpropanoylamino)-[1,2,4]triazolo[1,5-a]pyridin-7-yl]-N-[(1S)-1-phenylethyl]indole-3-carboxamide (3CI)
Ligand formula: C28 H28 N6 O2
Ligand molecular weight: 480.561
Ligand SMILES: CC(C)C(=O)Nc1nc2cc(ccn2n1)c3ccc4c(c3)c(cn4C)C(=O)NC(C)c5ccccc5
Ligand InChI: InChI=1S/C28H28N6O2/c1-17(2)26(35)31-28-30-25-15-21(12-13-34(25)32-28)20-10-11-24-22(14-20)23(16-33(24)4)27(36)29-18(3)19-8-6-5-7-9-19/h5-18H,1-4H3,(H,29,36)(H,31,32,35)/t18-/m0/s1
Release date: 2023-04-19
Human Carbonic Anhydrase II in complex with 4-Butylbenzenesulfonamide (PDB entry 6I3E)
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): 1.07
R work: 0.1292
R free: 0.1465
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: Trisodium citrate dihydrate 1.40 M, Tris 0.1 M, pH = 7.8, saturated with para-Chloromercuribenzoic acid.
Matthews coefficient: 2.06
Solvent content (%): 40.41
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2019-11-20
Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated POLR2A peptide (K775ac/K778ac) (PDB entry 6G0R)
Macromolecule: Bromodomain-containing protein 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 127 residues
Sequence: SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.1497
R free: 0.1749
Average B factor: 16.758
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 20.0 % PEG 6K
10.0 % EtGly
0.1 M HEPES pH 7.0                                0.1 M MgCl2
Matthews coefficient: 2.08
Solvent content (%): 40.81
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: 2018-11-28
LTA4 hydrolase in complex with compound3 (PDB entry 8RX9)
Macromolecule: Leukotriene A-4 hydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 613 residues
Sequence: GPGPEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPDVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2634
R free: 0.3349
Average B factor: 55
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 8000, 0.1 IMIDAZOLE PH 6.8, 0.1 SODIUM ACETATE, 0.005 M YBCL3
Matthews coefficient: 2.45
Solvent content (%): 49.89
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: 2024-03-20