satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of chromodomain of CDYL in complex with inhibitor UNC6261 (PDB entry 7N27)
Macromolecule: Isoform 2 of Chromodomain Y-like protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1
Sequence length: 57 residues
Sequence: GEELYEVERIVDKRKNKKGKTEYLVRWKGYDSEDDTWEPEQHLVNCEEYIHDFNRRH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.225
R free: 0.262
Average B factor: 31.01
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 3.5M Na Formate, 0.1M Bis-Tris propane pH7.0
Matthews coefficient: 2.01
Solvent content (%): 38.76
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2021-07-21
Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA<sub>2</sub>) Discovered Through X-Ray Fragment Screening (PDB entry 5JAT)
Macromolecule: Platelet-activating factor acetylhydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.47
Sequence length: 388 residues
Sequence: MAAASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTTNQHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.14
R free: 0.199
Average B factor: 29.655
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 28.0%w/v PEG 3350, 0.1M HEPES/NaOHpH=7.4, 1.3M NaCl
Matthews coefficient: 2.46
Solvent content (%): 50.06
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2016-05-25
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000072a (PDB entry 5QDL)
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): 1.833
R work: 0.1901
R free: 0.2118
Average B factor: 44.7659
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: 3.33
Solvent content (%): 63.02
Ligand: methyl 2-(4-aminophenoxy)benzoate (JFV)
Ligand formula: C14 H13 N O3
Ligand molecular weight: 243.258
Ligand SMILES: COC(=O)c1ccccc1Oc2ccc(cc2)N
Ligand InChI: InChI=1S/C14H13NO3/c1-17-14(16)12-4-2-3-5-13(12)18-11-8-6-10(15)7-9-11/h2-9H,15H2,1H3
Release date: 2018-10-10
CRYSTAL STRUCTURE OF BRUTON'S TYROSINE KINASE IN COMPLEX WITH INHIBITOR CGI2815 (PDB entry 6AUB)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 264 residues
Sequence: WEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.166
R free: 0.199
Average B factor: 21.1996
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 289
Crystal growth procedure: 100 MM IMIDAZOLE PH 7.0, 14% PEG 10,000, 200 MM LI2SO4, 10 MM BETA MERCAPTOETHANOL, 0.75% (W/V) s-BOG
Matthews coefficient: 2.31
Solvent content (%): 46.73
Ligand: 4-tert-butyl-N-[2-methyl-3-(1-methyl-5-{[5-(morpholine-4-carbonyl)pyridin-2-yl]amino}-6-oxo-1,6-dihydropyridin-3-yl)phenyl]benzamide (BXM)
Ligand formula: C34 H37 N5 O4
Ligand molecular weight: 579.689
Ligand SMILES: Cc1c(cccc1NC(=O)c2ccc(cc2)C(C)(C)C)C3=CN(C(=O)C(=C3)Nc4ccc(cn4)C(=O)N5CCOCC5)C
Ligand InChI: InChI=1S/C34H37N5O4/c1-22-27(7-6-8-28(22)37-31(40)23-9-12-26(13-10-23)34(2,3)4)25-19-29(33(42)38(5)21-25)36-30-14-11-24(20-35-30)32(41)39-15-17-43-18-16-39/h6-14,19-21H,15-18H2,1-5H3,(H,35,36)(H,37,40)
Release date: 2018-09-12
Crystal structure of the complex of Tdp1 with duplex DNA (PDB entry 5NW9)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 485 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMLEDPGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISYLTAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSALGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.2319
R free: 0.2709
Average B factor: 56.481
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 290
Crystal growth procedure: 0.1M Ammonium sulphate, 0.1M HEPES, 25% w/v PEG 8000
Matthews coefficient: 2.39
Solvent content (%): 48.51
Release date: 2018-01-10
Crystal Structure of human phosphodiesterase 10 in complex with 2-methyl-3-N-(2-phenylimidazo[1,2-a]pyrimidin-7-yl)-4-N-(1H-pyrazol-5-ylmethyl)pyrazole-3,4-dicarboxamide (PDB entry 5SF3)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1715
R free: 0.2236
Average B factor: 41.998
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.63
Solvent content (%): 53.3
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: 2022-10-12
DCN1 bound to inhibitor 10 (PDB entry 6XOP)
Macromolecule: Lysozyme, DCN1-like protein 1 chimera
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 386 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNAMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWAEAAVNLAKSRWYNQTPNRTKRVITTFATGTWDAYKNLRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.198
R free: 0.247
Average B factor: 30.95
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 28-33% PEG 3350, 0.2 M ammonium formate
Matthews coefficient: 2.09
Solvent content (%): 41.14
Ligand: N-[(1S)-1-cyclohexyl-2-{[(2S)-3-(1H-imidazol-1-yl)-2-methylpropanoyl]amino}ethyl]-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide (H9P)
Ligand formula: C31 H44 N6 O3 S
Ligand molecular weight: 580.784
Ligand SMILES: CCC(=O)NC(Cc1nc2ccc(cc2s1)C(C)C)C(=O)NC(CNC(=O)C(C)Cn3ccnc3)C4CCCCC4
Ligand InChI: InChI=1S/C31H44N6O3S/c1-5-28(38)34-25(16-29-35-24-12-11-23(20(2)3)15-27(24)41-29)31(40)36-26(22-9-7-6-8-10-22)17-33-30(39)21(4)18-37-14-13-32-19-37/h11-15,19-22,25-26H,5-10,16-18H2,1-4H3,(H,33,39)(H,34,38)(H,36,40)/t21-,25-,26+/m0/s1
Release date: 2021-06-02
Structure of the human JAK1 kinase domain with compound 21 (PDB entry 6N78)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 302 residues
Sequence: GDIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.234
R free: 0.261
Average B factor: 34.03
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M MES pH 5-6 and 25-35% PEG 6000
Matthews coefficient: 2.43
Solvent content (%): 49.29
Ligand: N-{3-[5-chloro-2-(difluoromethoxy)phenyl]-1-methyl-1H-pyrazol-4-yl}pyrazolo[1,5-a]pyrimidine-3-carboxamide (KEP)
Ligand formula: C18 H13 Cl F2 N6 O2
Ligand molecular weight: 418.785
Ligand SMILES: Cn1cc(c(n1)c2cc(ccc2OC(F)F)Cl)NC(=O)c3cnn4c3nccc4
Ligand InChI: InChI=1S/C18H13ClF2N6O2/c1-26-9-13(24-17(28)12-8-23-27-6-2-5-22-16(12)27)15(25-26)11-7-10(19)3-4-14(11)29-18(20)21/h2-9,18H,1H3,(H,24,28)
Release date: 2019-04-24
Protein Kinase A in complex with an Inhibitor (PDB entry 4UJB)
Macromolecule: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.11
Sequence length: 351 residues
Sequence: MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.949
R work: 0.1546
R free: 0.19
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 10MG/ML PROTEIN, 25MM BISTRIS/MES PH6.9, 50MM KCL, 1.5MM OCTANOYL-N-METHYLGLUCAMIDE, 1MM PROTEIN KINASE INHIBITOR PEPTIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Matthews coefficient: 2.56
Solvent content (%): 52.03
Ligand: 7-[(3S,4R)-4-(3-fluorophenyl)carbonylpyrrolidin-3-yl]-3H-quinazolin-4-one (8BQ)
Ligand formula: C19 H16 F N3 O2
Ligand molecular weight: 337.348
Ligand SMILES: c1cc(cc(c1)F)C(=O)C2CNCC2c3ccc4c(c3)N=CNC4=O
Ligand InChI: InChI=1S/C19H16FN3O2/c20-13-3-1-2-12(6-13)18(24)16-9-21-8-15(16)11-4-5-14-17(7-11)22-10-23-19(14)25/h1-7,10,15-16,21H,8-9H2,(H,22,23,25)/t15-,16+/m1/s1
Release date: 2016-04-13
Crystal structure of the tandem bromodomain (BD1, BD2) of human TAF1 bound to ATR inhibitor AZ20 (PDB entry 7K27)
Macromolecule: Transcription initiation factor TFIID subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 265 residues
Sequence: SMSIHRRRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELESLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1597
R free: 0.1753
Average B factor: 28.7846
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Matthews coefficient: 2.46
Solvent content (%): 50.03
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: 2021-09-22
Human Cyclophilin D in complex with N-cyclopentyl-N'-pyridin-2-ylmethyl-oxalamide (PDB entry 6R9X)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.144
R free: 0.193
Average B factor: 10.54
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: PEG4000
Matthews coefficient: 2.15
Solvent content (%): 42.92
Ligand: ~{N}'-cyclopentyl-~{N}-(pyridin-2-ylmethyl)ethanediamide (JW2)
Ligand formula: C13 H17 N3 O2
Ligand molecular weight: 247.293
Ligand SMILES: c1ccnc(c1)CNC(=O)C(=O)NC2CCCC2
Ligand InChI: InChI=1S/C13H17N3O2/c17-12(13(18)16-10-5-1-2-6-10)15-9-11-7-3-4-8-14-11/h3-4,7-8,10H,1-2,5-6,9H2,(H,15,17)(H,16,18)
Release date: 2019-11-27
Crystal structure of SETDB1 with a modified H3 peptide (PDB entry 6BHD)
Macromolecule: Histone-lysine N-methyltransferase SETDB1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 239 residues
Sequence: MHHHHHHSSGRENLYFQGGELSKDGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYDYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSMKTSSASALE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.1474
R free: 0.1829
Average B factor: 16.006
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol
Matthews coefficient: 2.32
Solvent content (%): 47.01
Ligand: UNKNOWN ATOM OR ION (UNX)
Ligand formula: X
Ligand SMILES: *
Release date: 2017-12-06
MELK in complex with NVS-MELK12B (PDB entry 5IHC)
Macromolecule: Maternal embryonic leucine zipper kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 335 residues
Sequence: MDYDELLKYYELHETIGTGGFAKVKLACHILTGEMVAIKIMDKNTLGSDLPRIKTEIEALKNLRHQHICQLYHVLETANKIFMVLEYCPGGELFDYIISQDRLSEEETRVVFRQIVSAVAYVHSQGYAHRDLKPENLLFDEYHKLKLIDFGLCAKPKGNKDYHLQTCCGSLAYAAPELIQGKSYLGSEADVWSMGILLYVLMCGFLPFDDDNVMALYKKIMRGKYDVPKWLSPSSILLLQQMLQVDPKKRISMKNLLNHPWIMQDYNYPVEWQSKNPFIHLDDDCVTELSVHHRNNRQTMEDLISLWQYDHLTATYLLLLAKKARGKPVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.1779
R free: 0.2084
Average B factor: 55.08
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 100mM Hepes, pH 7.6, 0.2M NaCl, 4.5-16.5% PEG3350
Matthews coefficient: 2.59
Solvent content (%): 52.56
Ligand: 4-[1-(2-fluorophenyl)-1H-pyrazol-4-yl]-3-[(piperidin-4-yl)methoxy]pyridine (6BB)
Ligand formula: C20 H21 F N4 O
Ligand molecular weight: 352.405
Ligand SMILES: c1ccc(c(c1)n2cc(cn2)c3ccncc3OCC4CCNCC4)F
Ligand InChI: InChI=1S/C20H21FN4O/c21-18-3-1-2-4-19(18)25-13-16(11-24-25)17-7-10-23-12-20(17)26-14-15-5-8-22-9-6-15/h1-4,7,10-13,15,22H,5-6,8-9,14H2
Release date: 2016-06-01
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOMB000293a (PDB entry 5QFP)
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): 1.771
R work: 0.2027
R free: 0.2285
Average B factor: 50.0446
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: 3.37
Solvent content (%): 63.45
Ligand: 3,4,6,7-tetrahydroacridine-1,8(2H,5H)-dione (JJY)
Ligand formula: C13 H13 N O2
Ligand molecular weight: 215.248
Ligand SMILES: c1c2c(nc3c1C(=O)CCC3)CCCC2=O
Ligand InChI: InChI=1S/C13H13NO2/c15-12-5-1-3-10-8(12)7-9-11(14-10)4-2-6-13(9)16/h7H,1-6H2
Release date: 2018-10-10
Human DDAH1 soaked with its inactivator S-((4-chloropyridin-2-yl)methyl)-L-cysteine (PDB entry 7ULV)
Macromolecule: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.3.18
Sequence length: 308 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASMAGLGHPAAFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTCCSVLINKKVDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.37
R work: 0.237
R free: 0.2692
Average B factor: 45.4034
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: Purified DDAH1 was concentrated to approximately 10 mg/mL using an Amicon-Ultra centrifugal filter device (10 kDa MWCO). The protein was crystallized at 25 C using the hanging drop method (Hampton Research, Aliso Viejo, CA) from 25 % (w/v) PEG6000, 0.1 M Tris-HCl, pH 8.2. Further optimization was done manually using a 1:1 well solution: DDAH1 stock solution ratio to improve crystal size and morphology.  Crystals grew to their maximum size in 3 weeks and were harvested after approximately 25 days. To determine the structure of DDAH1 in complex with ligand, the crystals were transferred to a reservoir containing 20 uL of 20 mM of the ligand in the crystallization mother liquor (25% PEG 6000, 0.1 M Tris-HCl, pH 8.2) and soaked for 30 min. Before data collection, crystals with good size and morphology were transferred into a cryoprotection solution (Well Solution supplemented with 25 % (v/v) glycerol) for 1 to 5 seconds using a the cryoloop (Hampton Research, Laguna Niguel, CA). Individual hDDAH1:ligand crystals were flash frozen in liquid nitrogen before use.
Matthews coefficient: 1.87
Solvent content (%): 34.27
Ligand: S-[(pyridin-2-yl)methyl]-L-cysteine (NO6)
Ligand formula: C9 H12 N2 O2 S
Ligand molecular weight: 212.269
Ligand SMILES: c1ccnc(c1)CSCC(C(=O)O)N
Ligand InChI: InChI=1S/C9H12N2O2S/c10-8(9(12)13)6-14-5-7-3-1-2-4-11-7/h1-4,8H,5-6,10H2,(H,12,13)/t8-/m0/s1
Release date: 2023-08-30
Structure of Maternal Embryonic Leucine Zipper Kinase (PDB entry 5TX3)
Macromolecule: Maternal embryonic leucine zipper kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 344 residues
Sequence: GSGSMKDYDELLKYYELHETIGTGGFAKVKLACHILTGEMVAIKIMDKNTLGSDLPRIKTEIEALKNLRHQHICQLYHVLETANKIFMVLEYCPGGELFDYIISQDRLSEEETRVVFRQIVSAVAYVHSQGYAHRDLKPENLLFDEYHKLKLIDFGLCAKPKGNKDYHLQTCCGSLAYAAPELIQGKSYLGSEADVWSMGILLYVLMCGFLPFDDDNVMALYKKIMRGKYDVPKWLSPSSILLLQQMLQVDPKKRISMKNLLNHPWIMQDYNYPVEWQSKNPFIHLDDDCVTELSVHHRNNRQTMEDLISLWQYDHLTATYLLLLAKKARGKPVRLRLSSFSCG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.1818
R free: 0.2528
Average B factor: 88.09
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 4000
Matthews coefficient: 2.36
Solvent content (%): 47.98
Ligand: 7-[(1S)-4-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-2-({3-[(pyrrolidin-1-yl)methyl]phenyl}amino)-5,7-dihydro-6H-pyrrolo[2,3-d]pyrimidin-6-one (7MY)
Ligand formula: C28 H31 N5 O2
Ligand molecular weight: 469.578
Ligand SMILES: CC1(c2cnc(nc2N(C1=O)C3CCc4c3cccc4O)Nc5cccc(c5)CN6CCCC6)C
Ligand InChI: InChI=1S/C28H31N5O2/c1-28(2)22-16-29-27(30-19-8-5-7-18(15-19)17-32-13-3-4-14-32)31-25(22)33(26(28)35)23-12-11-21-20(23)9-6-10-24(21)34/h5-10,15-16,23,34H,3-4,11-14,17H2,1-2H3,(H,29,30,31)/t23-/m0/s1
Release date: 2017-11-22
Structure of human ASF1a in complex with a TLK2 peptide (PDB entry 7LO0)
Macromolecule: Histone chaperone ASF1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 157 residues
Sequence: GSMAKVQVNNVVVLDNPSPFYNPFQFEITFECIEDLSEDLEWKIIYVGSAESEEYDQVLDSVLVGPVPAGRHMFVFQADAPNPGLIPDADAVGVTVVLITCTYRGQEFIRVGYYVNNEYTETELRENPPVKPDFSKLQRNILASNPRVTRFHINWED
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.71
R work: 0.213
R free: 0.2256
Average B factor: 63.0621
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 18% PEG3350, 0.2 M of trisodium citrate, pH 5.6 and 2% Octyl-D-glucose
Matthews coefficient: 3.25
Solvent content (%): 62.2
Release date: 2022-02-16
Crystal structure of human tryptophan hydroxylase 1 in complex with inhibitor KM-05-060 (PDB entry 7ZIG)
Macromolecule: Tryptophan 5-hydroxylase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.16.4
Sequence length: 326 residues
Sequence: MKHHHHHHHGAAGTSLYKKAGENLYFQGSVPWFPKKISDLDHCANRVLMYGSELDADHPGFKDNVYRKRRKYFADLAMNYKHGDPIPKVEFTEEEIKTWGTVFQELNKLYPTHACREYLKNLPLLSKYCGYREDNIPQLEDVSNFLKERTGFSIRPVAGYLSPRDFLSGLAFRVFHCTQYVRHSSDPFYTPEPDTCHELLGHVPLLAEPSFAQFSQEIGLASLGASEEAVQKLATCYFFTVEFGLCKQDGQLRVFGAGLLSSISELKHALSGHAKVKPFDPKITCKQECLITTFQDVYFVSESFEDAKEKMREFTKTIKRPFGVKY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.80888497598
R work: 0.167897277025
R free: 0.206340566536
Average B factor: 27.1641098215
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 26% w/v PEG 5000 MME, 200 mM ammonium sulfate, 100 mM Hepes-NaOH pH 7.0
Matthews coefficient: 2.15
Solvent content (%): 42.91
Ligand: (2~{R})-2-azanyl-5-[[2-[[3-methyl-2,6-bis(oxidanylidene)-7-(phenylmethyl)purin-8-yl]methyl]-1~{H}-benzimidazol-5-yl]amino]-5-oxidanylidene-pentanoic acid (IVZ)
Ligand formula: C26 H26 N8 O5
Ligand molecular weight: 530.535
Ligand SMILES: CN1c2c(n(c(n2)Cc3[nH]c4ccc(cc4n3)NC(=O)CCC(C(=O)O)N)Cc5ccccc5)C(=O)NC1=O
Ligand InChI: InChI=1S/C26H26N8O5/c1-33-23-22(24(36)32-26(33)39)34(13-14-5-3-2-4-6-14)20(31-23)12-19-29-17-9-7-15(11-18(17)30-19)28-21(35)10-8-16(27)25(37)38/h2-7,9,11,16H,8,10,12-13,27H2,1H3,(H,28,35)(H,29,30)(H,37,38)(H,32,36,39)/t16-/m1/s1
Release date: 2022-09-07