satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor (S)-2-(((1r,4S)-4-(4-amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclohexyl)amino)-4-methylpentanamide (PDB entry 5H0E)
Macromolecule: Tyrosine-protein kinase HCK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 454 residues
Sequence: GAMGSGIRIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLETEEWFFKGISRKDAERQLLAPGNMLGSFMIRDSETTKGSYSLSVRDYDPRQGDTVKHYKIRTLDNGGFYISPRSTFSTLQELVDHYKKGNDGLCQKLSVPCMSSKPQKPWEKDAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPGSMSVEAFLAEANVMKTLQHDKLVKLHAVVTKEPIYIITEFMAKGSLLDFLKSDEGSKQPLPKLIDFSAQIAEGMAFIEQRNYIHRDLRAANILVSASLVCKIADFGLARVIEDNEYTAREGAKFPIKWTAPEAINFGSFTIKSDVWSFGILLMEIVTYGRIPYPGMSNPEVIRALERGYRMPRPENCPEELYNIMMRCWKNRPEERPTFEYIQSVLDDFYTATESQYEEIP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.185
R free: 0.2255
Average B factor: 49.7425
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.22-0.25M ammonium formate, 12-22% PEG 3350
Matthews coefficient: 2.31
Solvent content (%): 46.66
Ligand: (2~{S})-2-[[4-[4-azanyl-5-(4-phenoxyphenyl)pyrrolo[2,3-d]pyrimidin-7-yl]cyclohexyl]amino]-4-methyl-pentanamide (OOS)
Ligand formula: C30 H36 N6 O2
Ligand molecular weight: 512.646
Ligand SMILES: CC(C)CC(C(=O)N)NC1CCC(CC1)n2cc(c3c2ncnc3N)c4ccc(cc4)Oc5ccccc5
Ligand InChI: InChI=1S/C30H36N6O2/c1-19(2)16-26(29(32)37)35-21-10-12-22(13-11-21)36-17-25(27-28(31)33-18-34-30(27)36)20-8-14-24(15-9-20)38-23-6-4-3-5-7-23/h3-9,14-15,17-19,21-22,26,35H,10-13,16H2,1-2H3,(H2,32,37)(H2,31,33,34)/t21-,22-,26-/m0/s1
Release date: 2017-10-04
Crystal structure of human NatD (NAA40) bound to a bisubstrate analogue (PDB entry 7KD7)
Macromolecule: SER-GLY-ARG-GLY-LYS
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 5 residues
Sequence: SGRGK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.1614
R free: 0.1829
Average B factor: 25.74
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM BIS-TRIS pH 5.5, 2000 mM Ammonium sulfate
Matthews coefficient: 2.27
Solvent content (%): 45.88
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: 2021-06-16
ATAD2 in complex with FragLite2 (PDB entry 7QUM)
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): 1.5
R work: 0.1973
R free: 0.2233
Average B factor: 32.315
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2023-03-01
Crystal structure of human TATDN1 bound to dAMP and two zinc ions (PDB entry 8EFG)
Macromolecule: Deoxyribonuclease TATDN1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.21
Sequence length: 295 residues
Sequence: SRFKFIDIGINLTDPMFRGIYRGVQKHQDDLQDVIGRAVEIGVKKFMITGGNLQDSKDALHLAQTNGMFFSTVGCHPTRCGEFEKNNPDLYLKELLNLAENNKGKVVAIGECGLDFDRLQFCPKDTQLKYFEKQFELSEQTKLPMFLHCRNSHAEFLDIMKRNRDRCVGGVVHSFDGTKEAAAALIDLDLYIGFNGCSLKTEANLEVLKSIPSEKLMIETDAPWCGVKSTHAGSKYIRTAFPTKKKWESGHCLKDRNEPCHIIQILEIMSAVRDEDPLELANTLYNNTIKVFFPG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1627
R free: 0.1888
Average B factor: 23.162
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 19% PEG 8000, 100 mM HEPES pH 7.0
Matthews coefficient: 2.44
Solvent content (%): 49.7
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: 2023-02-22
Crystal structure of human MAP4K1 with an inhibitor, BAY-405 (PDB entry 8PAR)
Macromolecule: Mitogen-activated protein kinase kinase kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 308 residues
Sequence: GMDVVDPDIFNRDPRDHYDLLQRLGGGTYGEVFKARDKVSGDLVALKMVKMEPDDDVSTLQKEILILKTCRHANIVAYHGSYLWLQKLWICMEFCGAGSLQDIYQVTGSLSELQISYVCREVLQGLAYLHSQKKIHRDIKGANILINDAGEVRLADFGISAQIGAELARRLEFIGTPYWMAPEVAAVALKGGYNELCDIWSLGITAIELAELQPPLFDVHPLRVLFLMTKSGYQPPRLKEKGKWSAAFHNFIKVTLTKSPKKRPSATKMLSHQLVSQPGLNRGLILDLLDKLKNPGKGPSIGDIEDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.23953
R free: 0.29244
Average B factor: 56.109
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M TRIS pH 8.0, 20 % MPD
Matthews coefficient: 2.21
Solvent content (%): 44.23
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: 2024-06-26
JAK2 Pseudokinase in complex with AZD7762 (PDB entry 5WIL)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 277 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1994
R free: 0.2312
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 200 mM Sodium Acetate, 100 mM Tris-HCl, 18%-30%(w/v) polyethylene glycol 4000.
Matthews coefficient: 2.5
Solvent content (%): 50.71
Ligand: 5-(3-fluorophenyl)-N-[(3S)-3-piperidyl]-3-ureido-thiophene-2-carboxamide (YDJ)
Ligand formula: C17 H19 F N4 O2 S
Ligand molecular weight: 362.422
Ligand SMILES: c1cc(cc(c1)F)c2cc(c(s2)C(=O)NC3CCCNC3)NC(=O)N
Ligand InChI: InChI=1S/C17H19FN4O2S/c18-11-4-1-3-10(7-11)14-8-13(22-17(19)24)15(25-14)16(23)21-12-5-2-6-20-9-12/h1,3-4,7-8,12,20H,2,5-6,9H2,(H,21,23)(H3,19,22,24)/t12-/m0/s1
Release date: 2018-08-01
FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl [(4R,5E,8S)-8-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-4-methyl-2-oxo-1,3,4,7,8,10-hexahydro-2H-12,9-(azeno)-1,10-benzodiazacyclotetradecin-15-yl]carbamate (PDB entry 5Q0F)
Macromolecule: Coagulation factor XI
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.185
R free: 0.197
Average B factor: 29.9
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM sodium acetate, pH 4.6, 25% (w/v) MePEG2000, 200 mM ammonium sulfate, then transferred to 100 mM Tris-HCl, pH 7.0, 25% (w/v) MePEG2000, 200 MM ammonium sulfate
Matthews coefficient: 3.18
Solvent content (%): 61.27
Ligand: methyl [(4R,5E,8S)-8-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-4-methyl-2-oxo-1,3,4,7,8,10-hexahydro-2H-12,9-(azeno)-1,10-benzodiazacyclotetradecin-15-yl]carbamate (9FA)
Ligand formula: C29 H28 Cl N9 O4
Ligand molecular weight: 602.044
Ligand SMILES: CC1CC(=O)Nc2cc(ccc2-c3c[nH]c(n3)C(CC=C1)NC(=O)C=Cc4cc(ccc4n5cnnn5)Cl)NC(=O)OC
Ligand InChI: InChI=1S/C29H28ClN9O4/c1-17-4-3-5-22(34-26(40)11-6-18-13-19(30)7-10-25(18)39-16-32-37-38-39)28-31-15-24(36-28)21-9-8-20(33-29(42)43-2)14-23(21)35-27(41)12-17/h3-4,6-11,13-17,22H,5,12H2,1-2H3,(H,31,36)(H,33,42)(H,34,40)(H,35,41)/b4-3+,11-6+/t17-,22-/m0/s1
Release date: 2017-07-12
Thrombin in complex with 1-amidinopiperidine (PDB entry 4UE7)
Macromolecule: THROMBIN HEAVY CHAIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 258 residues
Sequence: IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.129
R work: 0.1235
R free: 0.1394
Average B factor: 17.9
Crystallization pH: 7.5
Crystal growth procedure: SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
Matthews coefficient: 2.48
Solvent content (%): 50.49
Ligand: IODIDE ION (IOD)
Ligand formula: I
Ligand molecular weight: 126.904
Ligand SMILES: [I-]
Ligand InChI: InChI=1S/HI/h1H/p-1
Release date: 2015-08-26
Crystal structure of the catalytic domain of membrane type 1 matrix metalloproteinase (PDB entry 5H0U)
Macromolecule: Matrix metalloproteinase-14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.80
Sequence length: 170 residues
Sequence: GLKWQHNEITFCIQNYTPKVGEYATYEAIRKAFRVWESATPLRFREVPYAYIREGHEKQADIMIFFAEGFHGDSTPFDGEGGFLAHAYFPGPNIGGDTHFDSAEPWTVRNEDLNGNDIFLVAVHELGHALGLEHSSDPSAIMAPFYQWMDTENFVLPDDDRRGIQQLYGG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.239
R work: 0.1953
R free: 0.2538
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: Ammonium nitrate, PEG3350
Matthews coefficient: 3.04
Solvent content (%): 59.49
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2017-10-04
High-salt structure of protein kinase CK2 catalytic subunit with 4'-carboxy-6,8-bromo-flavonol (FLC26) showing an extreme distortion of the ATP-binding loop combined with a pi-halogen bond (PDB entry 4UB7)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 335 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1772
R free: 0.2187
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 4M sodium chloride
Matthews coefficient: 2.23
Solvent content (%): 44.79
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: 2015-07-01
Crystal structures of FNIII domain one and two of the human leucocyte common antigen-related protein, LAR (PDB entry 6TPV)
Macromolecule: Receptor-type tyrosine-protein phosphatase F
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 208 residues
Sequence: MHHHHHHENLYFQGPKPPIDLVVTETTATSVTLTWDSGNSEPVTYYGIQYRAAGTEGPFQEVDGVATTRYSIGGLSPFSEYAFRVLAVNSIGRGPPSEAVRARTGEQAPSSPPRRVQARMLSASTMLVQWEPPEEPNGLVRGYRVYYTPDSRRPPNAWHKHNTDAGLLTTVGSLLPGITYSLRVLAFTAVGDGPPSPTIQVKTQQGVP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1855
R free: 0.22
Average B factor: 41.93
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M Sodium citrate tribasic dihydrate pH 8.3, 20 % PEG 3,350
Matthews coefficient: 2.38
Solvent content (%): 48.24
Ligand: IMIDAZOLE (IMD)
Ligand formula: C3 H5 N2
Ligand molecular weight: 69.085
Ligand SMILES: c1c[nH+]c[nH]1
Ligand InChI: InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)/p+1
Release date: 2020-05-13
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000004a (PDB entry 5QDH)
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): 1.682
R work: 0.2371
R free: 0.2573
Average B factor: 34.1903
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.32
Solvent content (%): 62.99
Ligand: 1-(3-chlorophenyl)-N-methylmethanamine (JFJ)
Ligand formula: C8 H10 Cl N
Ligand molecular weight: 155.625
Ligand SMILES: CNCc1cccc(c1)Cl
Ligand InChI: InChI=1S/C8H10ClN/c1-10-6-7-3-2-4-8(9)5-7/h2-5,10H,6H2,1H3
Release date: 2018-10-10
Crystal structure of HLA-A*11:01 in complex with KRAS peptide (VVVGAGGVGK) (PDB entry 7OW3)
Macromolecule: MHC class I antigen
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 275 residues
Sequence: GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.46
R work: 0.22804
R free: 0.25954
Average B factor: 35.28
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000
Matthews coefficient: 2.57
Solvent content (%): 52.12
Release date: 2022-07-20
ZAP-70-tSH2:compound-A complex (PDB entry 4XZ0)
Macromolecule: Tyrosine-protein kinase ZAP-70
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 262 residues
Sequence: GPHMPDPAAHLPFFYGSISRAEAEEHLKLAGMADGLFLLRQCLRSLGGYVLSLVHDVRFHHFPIERQLNGTYAIAGGKAHCGPAELCEFYSRDPDGLPCNLRKPCNRPSGLEPQPGVFDCLRDAMVRDYVRQTWKLEGEALEQAIISQAPQVEKLIATTAHERMPWYHSSLTREEAERKLYSGAQTDGKFLLRPRKEQGTYALSLIYGKTVYHYLISQDKAGKYCIPEGTKFDTLWQLVEYLKLKADGLIYCLKEACPNSSA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2124
R free: 0.245
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, ammonium sulfate, TCEP
Matthews coefficient: 2.76
Solvent content (%): 55.45
Ligand: 1-(3-{5-[(3-chlorobenzyl)sulfonyl]-1H-tetrazol-1-yl}phenyl)ethanone (4N5)
Ligand formula: C16 H13 Cl N4 O3 S
Ligand molecular weight: 376.817
Ligand SMILES: CC(=O)c1cccc(c1)n2c(nnn2)S(=O)(=O)Cc3cccc(c3)Cl
Ligand InChI: InChI=1S/C16H13ClN4O3S/c1-11(22)13-5-3-7-15(9-13)21-16(18-19-20-21)25(23,24)10-12-4-2-6-14(17)8-12/h2-9H,10H2,1H3
Release date: 2015-06-17
Crystal structure of BACE complex withBMC006 (PDB entry 5QD0)
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): 2.6
R work: 0.165
R free: 0.207
Average B factor: 62.91
Crystallization method: hanging drop
Crystallization pH: 5
Crystallization temperature (K): 292
Crystal growth procedure: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS, FROM 1.0M AMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE, PH
5.0. PROTEIN STOCK WAS BACE MUT46B BATCH XIV 6.3MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 7-FOLD EXCESS OF BMC006
ADDED FROM A 50MM STOCK SOLUTION IN 90% DMSO-D6 (2.0% DMSO IN DROP). A SOLUTION CONTAINING 1.2M AMMONIUM PHOSPHATE, 0.1M
SODIUM CITRATE PH 5.0, 25% GLYCEROL, 1MM BMC006 AND 2.0% DMSO WAS USED AS CRYO-PROTECTANT.
Matthews coefficient: 2.91
Solvent content (%): 57.67
Ligand: (5S,8S,10R)-8-[(1R)-1-hydroxy-2-{[(5-propyl-1H-pyrazol-3-yl)methyl]amino}ethyl]-4,5,10-trimethyl-1-oxa-4,7-diazacyclohexadecane-3,6-dione (E5Y)
Ligand formula: C25 H45 N5 O4
Ligand molecular weight: 479.656
Ligand SMILES: CCCc1cc(n[nH]1)CNCC(C2CC(CCCCCCOCC(=O)N(C(C(=O)N2)C)C)C)O
Ligand InChI: InChI=1S/C25H45N5O4/c1-5-10-20-14-21(29-28-20)15-26-16-23(31)22-13-18(2)11-8-6-7-9-12-34-17-24(32)30(4)19(3)25(33)27-22/h14,18-19,22-23,26,31H,5-13,15-17H2,1-4H3,(H,27,33)(H,28,29)/t18-,19+,22+,23-/m1/s1
Release date: 2020-06-03
Structure-based optimization of 1H-imidazole-2-carboxamides as Axl kinase inhibitors utilizing a Mer mutant surrogate (PDB entry 5TC0)
Macromolecule: Tyrosine-protein kinase Mer
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 314 residues
Sequence: MGSSHHHHHHSSGLVPRGSSEELQNKLEDVVIDRNLLILGKILGEGEFGSVMEGNLKQEDGTSLKVAVKTMKLDNSSQREIEEFLSEAACMKDFSHPNVMRLLGVCIEMSSQGIPKPMVILPFMKYGDLHTYLLYSRLETGPKHIPLQTLLKFMVDIALGMEYLSNRNFLHRDLAARNCMLRDDMTVCVADFGLSKKIYSGDYYRQGRIAKMPVKWIAIESLADRVYTSKSDVWAFGVTMWEIATRGMTPYPGVQNHEMYDYLLHGHRLKQPEDCLDELYEIMYSCWRTDPLDRPTFSVLRLQLEKLLESLPDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.2275
R free: 0.2624
Average B factor: 56.147
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 29% PEG 400, 0.2M MgCl2, 0,1M Tris pH 8.5
Matthews coefficient: 2.2
Solvent content (%): 44.03
Ligand: N-(2-{4-[(2S)-4-(methylsulfonyl)morpholin-2-yl]-1,3-thiazol-2-yl}phenyl)-1H-imidazole-2-carboxamide (79Y)
Ligand formula: C18 H19 N5 O4 S2
Ligand molecular weight: 433.505
Ligand SMILES: CS(=O)(=O)N1CCOC(C1)c2csc(n2)c3ccccc3NC(=O)c4[nH]ccn4
Ligand InChI: InChI=1S/C18H19N5O4S2/c1-29(25,26)23-8-9-27-15(10-23)14-11-28-18(22-14)12-4-2-3-5-13(12)21-17(24)16-19-6-7-20-16/h2-7,11,15H,8-10H2,1H3,(H,19,20)(H,21,24)/t15-/m0/s1
Release date: 2017-01-25
Notum Inhibitor ARUK3004876 (PDB entry 8BT2)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1983
R free: 0.2226
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.2
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.93
Solvent content (%): 36.23
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: 2022-12-14
Crystal structure of human Sirt2 in complex with a triazole-based SirReal (PDB entry 8OWZ)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 304 residues
Sequence: GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1683
R free: 0.1975
Average B factor: 27.04
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 25 % PEG 3,350 , 0.1 M Bis-Tris pH 6.5
Matthews coefficient: 2.11
Solvent content (%): 41.58
Ligand: 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-N-[5-[[3-[[1-(2-methoxyethyl)-1,2,3-triazol-4-yl]methoxy]phenyl]methyl]-1,3-thiazol-2-yl]ethanamide (KZU)
Ligand formula: C24 H27 N7 O3 S2
Ligand molecular weight: 525.646
Ligand SMILES: Cc1cc(nc(n1)SCC(=O)Nc2ncc(s2)Cc3cccc(c3)OCc4cn(nn4)CCOC)C
Ligand InChI: InChI=1S/C24H27N7O3S2/c1-16-9-17(2)27-24(26-16)35-15-22(32)28-23-25-12-21(36-23)11-18-5-4-6-20(10-18)34-14-19-13-31(30-29-19)7-8-33-3/h4-6,9-10,12-13H,7-8,11,14-15H2,1-3H3,(H,25,28,32)
Release date: 2023-11-15
Structure of cathepsin K in complex with the 3-cyano-3-aza-beta-amino acid inhibitor Gu2602 (PDB entry 7QBL)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 215 residues
Sequence: APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2173
R free: 0.2858
Average B factor: 34.95
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 10% PEG 8000, 20% ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.1 M MES/imidazole pH 6.5
Matthews coefficient: 1.84
Solvent content (%): 33.13
Ligand: ~{tert}-butyl ~{N}-[iminomethyl-[2-[methyl-(phenylmethyl)amino]-2-oxidanylidene-ethyl]amino]carbamate (A0U)
Ligand formula: C16 H24 N4 O3
Ligand molecular weight: 320.387
Ligand SMILES: CC(C)(C)OC(=O)NN(CC(=O)N(C)Cc1ccccc1)C=N
Ligand InChI: InChI=1S/C16H24N4O3/c1-16(2,3)23-15(22)18-20(12-17)11-14(21)19(4)10-13-8-6-5-7-9-13/h5-9,12,17H,10-11H2,1-4H3,(H,18,22)/b17-12+
Release date: 2022-01-26