satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human tankyrase 2 in complex with TA-47 (PDB entry 4UI6)
Macromolecule: TANKYRASE-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 48 residues
Sequence: MAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.15371
R free: 0.18555
Average B factor: 22.743
Crystallization pH: 8.5
Crystal growth procedure: 0.2 M LISO4, 0.1 M TRIS HCL, 22% PEG3350, PH 8.5
Matthews coefficient: 2.4
Solvent content (%): 50
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: 2016-04-13
Structure of compound 1 bound KMT9 (PDB entry 8CNC)
Macromolecule: Methyltransferase N6AMT1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 203 residues
Sequence: SHVGRGAFSDVYEPAEDTFLLLDALEAAAAELAGVEICLEVGSGSGVVSAFLASMIGPQALYMCTDINPEAAACTLETARCNKVHIQPVITDLVKGLLPRLTEKVDLLVFNPPYVVTPPQEVGSHGIEAAWAGGRNGREVMDRFFPLVPDLLSPRGLFYLVTIKENNPEEILKIMKTKGLQGTTALSRQAGQETLSVLKFTKS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.15179
R free: 0.1833
Average B factor: 19.019
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M Na3Citrate, 0.1M Tris ph 8.0
Matthews coefficient: 3.16
Solvent content (%): 61.12
Ligand: 5'-{[(3S)-3-amino-3-carboxypropyl](3-aminopropyl)amino}-5'-deoxyadenosine (6D6)
Ligand formula: C17 H28 N8 O5
Ligand molecular weight: 424.455
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCCN)CCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C17H28N8O5/c18-3-1-4-24(5-2-9(19)17(28)29)6-10-12(26)13(27)16(30-10)25-8-23-11-14(20)21-7-22-15(11)25/h7-10,12-13,16,26-27H,1-6,18-19H2,(H,28,29)(H2,20,21,22)/t9-,10+,12+,13+,16+/m0/s1
Release date: 2024-03-06
Crystal structure of JAK1 in complex with PF-4950736 (PDB entry 5KHX)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 316 residues
Sequence: GSIMRDINKLEEQNPDIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1703
R free: 0.2416
Average B factor: 49.99
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 30% PEG 1500, 8% MPD, 0.1 M Tris pH 9.0
Matthews coefficient: 2.06
Solvent content (%): 40.24
Ligand: ~{N}-[3-[methyl(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)amino]cyclobutyl]methanesulfonamide (6TE)
Ligand formula: C12 H17 N5 O2 S
Ligand molecular weight: 295.361
Ligand SMILES: CN(c1c2cc[nH]c2ncn1)C3CC(C3)NS(=O)(=O)C
Ligand InChI: InChI=1S/C12H17N5O2S/c1-17(9-5-8(6-9)16-20(2,18)19)12-10-3-4-13-11(10)14-7-15-12/h3-4,7-9,16H,5-6H2,1-2H3,(H,13,14,15)/t8-,9+
Release date: 2016-11-09
Human DDAH-1, apo form (PDB entry 7UT0)
Macromolecule: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.3.18
Sequence length: 286 residues
Sequence: GAAGLGHPAAFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTCCSVLINKKVDS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.68
R work: 0.1511
R free: 0.2079
Average B factor: 27.3175
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM Tris-HCl (pH 8.5), 300 mM sodium acetate, 21% PEG6000
Matthews coefficient: 2.29
Solvent content (%): 46.19
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: 2022-05-18
Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Compound 5 (PDB entry 5C7B)
Macromolecule: E3 ubiquitin-protein ligase XIAP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 110 residues
Sequence: GSHMNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.20248
R free: 0.26489
Average B factor: 39.172
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Hepes-NaOH 7.5, 3.9M NaCl
Matthews coefficient: 2.32
Solvent content (%): 47
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: 2015-08-12
Crystal structure of human MST2 in complex with SAV1 SARAH domain (PDB entry 6AO5)
Macromolecule: Serine/threonine-protein kinase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 362 residues
Sequence: EDSLTKQPEEVFDVLEKLGEGSYGSVFKAIHKESGQVVAIKQVPVESDLQEIIKEISIMQQCDSPYVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLRNKTLIEDEIATILKSTLKGLEYLHFMRKIHRNIKAGNILLNTEGHAKLADFGVAGQLTDTMAKRNTVIGTPFWMAPEVIQEIGYNCVADIWSLGITSIEMAEGKPPYADIHPMRAIFMIPTNPPPTFRKPELWSDDFTDFVKKCLVKNPEQRATATQLLQHPFIKNAKPVSILRDLITEAMEIKAKRHEEQQRELEEEENWKVPQDGDFDFLKNLSLEELQMRLKALDPMMEREIEELRQRYTAKRQPILDAMDAKKRRQQNF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.955
R work: 0.2346
R free: 0.2564
Average B factor: 60.0404
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.05 M NaCl, 0.1 M Hepes, 0.19 mM CYMAL-7, 1 mM TCEP, 40% PEG 400
Matthews coefficient: 3.62
Solvent content (%): 65.99
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2017-11-08
LIM Domain Kinase 1 (LIMK1) bound to LIMKi3 (PDB entry 8AAU)
Macromolecule: LIM domain kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 310 residues
Sequence: SMPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKVMRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASGMAYLHSMNIIHRDLNSHNCLVRENKNVVVADFGLARLMVDEKTQPEGLRSLKKPDRKKRYTVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFLDRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQLDRGFWETYRRGES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.2114
R free: 0.2399
Average B factor: 40.7
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M acetate pH 4.5, 0.2 M lithium sulfate, 12% PEG8K
Matthews coefficient: 2.84
Solvent content (%): 56.76
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: 2022-08-10
Structural Investigations of the Substrate Specificity of Human O-GlcNAcase (PDB entry 5VVX)
Macromolecule: Protein O-GlcNAcase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.169
Sequence length: 504 residues
Sequence: HFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDNIDHNMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRKDVVMTDSEDSTVSIQIKLENEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSRGGGGSGGGGSVTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSVVSVNCKGKDSEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRSHSSAQFLIGDQEPWAFRGGLAGEFQRLLPIDGANDLFFQ
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.19988
R free: 0.28221
Average B factor: 88.838
Crystallization method: EVAPORATION
Crystallization temperature (K): 293
Crystal growth procedure: 0.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9.6 % w/v polyethylene glycol 3,350, 2.4 % w/v polyethylene glycol monomethyl ether 2,000, and 4% w/v polyethylene glycol monomethyl ether 550
Matthews coefficient: 2.74
Solvent content (%): 55.16
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: 2017-09-27
High-resolution crystal structure of ERAP1 in complex with 15mer phosphinic peptide (PDB entry 6RYF)
Macromolecule: Endoplasmic reticulum aminopeptidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11
Sequence length: 894 residues
Sequence: PFPWNKIRLPEYVIPVHYDLLIHANLTTLTFWGTTKVEITASQPTSTIILHSHHLQISRATLRKGAGERLSEEPLQVLEHPRQEQIALLAPEPLLVGLPYTVVIHYAGNLSETFHGFYKSTYRTKEGELRILASTQFEPTAARMAFPCFDEPAFKASFSIKIRREPRHLAISNMPLVKSVTVAEGLIEDHFDVTVKMSTYLVAFIISDFESVSKITKSGVKVSVYAVPDKINQADYALDAAVTLLEFYEDYFSIPYPLPKQDLAAIPDFQSGAMENWGLTTYRESALLFDAEKSSASSKLGITMTVAHELAHQWFGNLVTMEWWNDLWLNEGFAKFMEFVSVSVTHPELKVGDYFFGKCFDAMEVDALNSSHPVSTPVENPAQIREMFDDVSYDKGACILNMLREYLSADAFKSGIVQYLQKHSYKNTKNEDLWDSMASICPTDGVKGMDGFCSRSQHSSSSSHWHQEGVDVKTMMNTWTLQKGFPLITITVRGRNVHMKQEHYMKGSDGAPDTGYLWHVPLTFITSKSDMVHRFLLKTKTDVLILPEEVEWIKFNVGMNGYYIVHYEDDGWDSLTGLLKGTHTAVSSNDRASLINNAFQLVSIGKLSIEKALDLSLYLKHETEIMPVFQGLNELIPMYKLMEKRDMNEVETQFKAFLIRLLRDLIDKQTWTDEGSVSERMLRSQLLLLACVHNYQPCVQRAEGYFRKWKESNGNLSLPVDVTLAVFAVGAQSTEGWDFLYSKYQFSLSSTEKSQIEFALCRTQNKEKLQWLLDESFKGDKIKTQEFPQILTLIGRNPVGYPLAWQFLRKNWNKLVQKFELGSSSIAHMVMGTTNQFSTRTRLEEVKGFFSSLKENGSQLRCVQQTIETIEENIGWMDKNFDKIRVWLQSEKLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.1765
R free: 0.2013
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM propionic acid, cacodylate and Bis-tris propane pH 7.0, 25% PEG 1500
Matthews coefficient: 2.44
Solvent content (%): 49.69
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: 2019-12-18
Crystal structure of CHK1 kinase domain in complex with a CLASPIN phosphopeptide (PDB entry 7AKO)
Macromolecule: Serine/threonine-protein kinase Chk1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 300 residues
Sequence: GPGSAVPFVEDWRLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICINKMLNHENVVKFYGHRREGNIQYLFLEYCSGGELFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPENLLLDERDNLKISDFGLATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRPRVTSGGVSESPSGHHHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.19
R free: 0.2351
Average B factor: 40.63
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 287.15
Crystal growth procedure: 200 mM Sodium citrate tribasic dihydrate, 100 mM Bis-Tris propane pH 6.5 and 20% w/v PEG 3350
Matthews coefficient: 2.59
Solvent content (%): 52.47
Ligand: STAUROSPORINE (STU)
Ligand formula: C28 H26 N4 O3
Ligand molecular weight: 466.531
Ligand SMILES: CC12C(C(CC(O1)n3c4ccccc4c5c3c6n2c7ccccc7c6c8c5C(=O)NC8)NC)OC
Ligand InChI: InChI=1S/C28H26N4O3/c1-28-26(34-3)17(29-2)12-20(35-28)31-18-10-6-4-8-14(18)22-23-16(13-30-27(23)33)21-15-9-5-7-11-19(15)32(28)25(21)24(22)31/h4-11,17,20,26,29H,12-13H2,1-3H3,(H,30,33)/t17-,20-,26-,28+/m1/s1
Release date: 2021-04-14
Crystal structure of chimeric carbonic anhydrase XII with 2-(Cyclooctylamino)-3,5,6-trifluorobenzenesulfonamide (PDB entry 6YH6)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFKVEFDDSQDKAVLKGGPLDGTYRLTQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDAGKASQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLNECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1388
R free: 0.1971
Average B factor: 17.878
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE a
nd 3.4M sodium malonate
Matthews coefficient: 1.96
Solvent content (%): 37.2
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: 2021-04-07
Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD (PDB entry 7CJ0)
Macromolecule: Histone H3.3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 79 residues
Sequence: STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2577
R free: 0.2948
Average B factor: 81.1957
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol
Matthews coefficient: 2.67
Solvent content (%): 58.48
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: 2021-04-14
IRAK4 in complex with Compound 28 (PDB entry 5K76)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: VSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.74
R work: 0.217
R free: 0.246
Average B factor: 84.74
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 2.5 M ammonium sulfate, 0.1 M Hepes
Matthews coefficient: 2.95
Solvent content (%): 58.27
Ligand: ~{N}-(4-morpholin-4-ylcyclohexyl)-5-(oxan-4-yl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine (6R1)
Ligand formula: C21 H31 N5 O2
Ligand molecular weight: 385.503
Ligand SMILES: c1c(c2c([nH]1)ncnc2NC3CCC(CC3)N4CCOCC4)C5CCOCC5
Ligand InChI: InChI=1S/C21H31N5O2/c1-3-17(26-7-11-28-12-8-26)4-2-16(1)25-21-19-18(15-5-9-27-10-6-15)13-22-20(19)23-14-24-21/h13-17H,1-12H2,(H2,22,23,24,25)/t16-,17-
Release date: 2017-12-06
Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(2-(aminomethyl)-5-chlorobenzyl) pyrrolidine-2-carboxamide (PDB entry 5LPD)
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 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1492
R free: 0.1701
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM Sodium dihydrogen phosphate ph 7.5, 350 mM NaCl, 27% PEG 8000
Matthews coefficient: 2.5
Solvent content (%): 50
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: 2017-07-26
Crystal Structure Analysis of TAF1 Bromodomain (PDB entry 6P38)
Macromolecule: Transcription initiation factor TFIID subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 137 residues
Sequence: SMDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELESLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2058
R free: 0.2193
Average B factor: 103.5489
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 2000, Trimethylamine N-oxide dihydrate, Tris pH 8.5
Ligand: 4-{[(3R)-4-cyclopentyl-1,3-dimethyl-2-oxo-1,2,3,4-tetrahydropyrido[2,3-b]pyrazin-6-yl]amino}-N-(1-methylpiperidin-4-yl)-3-[(propan-2-yl)oxy]benzamide (NQV)
Ligand formula: C30 H42 N6 O3
Ligand molecular weight: 534.693
Ligand SMILES: CC1C(=O)N(c2ccc(nc2N1C3CCCC3)Nc4ccc(cc4OC(C)C)C(=O)NC5CCN(CC5)C)C
Ligand InChI: InChI=1S/C30H42N6O3/c1-19(2)39-26-18-21(29(37)31-22-14-16-34(4)17-15-22)10-11-24(26)32-27-13-12-25-28(33-27)36(23-8-6-7-9-23)20(3)30(38)35(25)5/h10-13,18-20,22-23H,6-9,14-17H2,1-5H3,(H,31,37)(H,32,33)/t20-/m1/s1
Release date: 2020-05-27
PDE4 crystal structure in complex with small molecule inhibitor (PDB entry 5K1I)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 326 residues
Sequence: TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.61
R work: 0.1913
R free: 0.2583
Average B factor: 30.959
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 19% PEG 3350, 36 % Ethylene Glycol and 10 % Isopropanol as a precipitant
Matthews coefficient: 2.59
Solvent content (%): 52.45
Ligand: 4-[(5-acetyl-2-ethyl-3-oxo-6-phenyl-2,3-dihydropyridazin-4-yl)amino]benzoic acid (6PT)
Ligand formula: C21 H19 N3 O4
Ligand molecular weight: 377.393
Ligand SMILES: CCN1C(=O)C(=C(C(=N1)c2ccccc2)C(=O)C)Nc3ccc(cc3)C(=O)O
Ligand InChI: InChI=1S/C21H19N3O4/c1-3-24-20(26)19(22-16-11-9-15(10-12-16)21(27)28)17(13(2)25)18(23-24)14-7-5-4-6-8-14/h4-12,22H,3H2,1-2H3,(H,27,28)
Release date: 2016-12-21
Anaplastic lymphoma kinase (ALK) catalytic domain complexed with novel inhibitor 3-sulfonylpyrazol-4-amino pyrimidine (PDB entry 5IMX)
Macromolecule: ALK tyrosine kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 327 residues
Sequence: MAHHHHHHNPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVEEEEKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.2105
R free: 0.2593
Average B factor: 48.517
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 18% PEG 3350, 0.1 M Tris-HCl, PH 8.5
Matthews coefficient: 2.08
Solvent content (%): 40.81
Ligand: 5-chloro-N~2~-{5-methyl-4-(1-methylpiperidin-4-yl)-2-[(propan-2-yl)oxy]phenyl}-N~4~-{1-methyl-3-[(propan-2-yl)sulfonyl]-1H-pyrazol-4-yl}pyrimidine-2,4-diamine (CZ4)
Ligand formula: C27 H38 Cl N7 O3 S
Ligand molecular weight: 576.154
Ligand SMILES: Cc1cc(c(cc1C2CCN(CC2)C)OC(C)C)Nc3ncc(c(n3)Nc4cn(nc4S(=O)(=O)C(C)C)C)Cl
Ligand InChI: InChI=1S/C27H38ClN7O3S/c1-16(2)38-24-13-20(19-8-10-34(6)11-9-19)18(5)12-22(24)31-27-29-14-21(28)25(32-27)30-23-15-35(7)33-26(23)39(36,37)17(3)4/h12-17,19H,8-11H2,1-7H3,(H2,29,30,31,32)
Release date: 2016-05-04
Crystal structure of TrkA (G595R) kinase domain (PDB entry 7VKM)
Macromolecule: Tyrosine-protein kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 326 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQGAMGSGIRVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHRDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.19893
R free: 0.25717
Average B factor: 60.159
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 3.0M NaCl, 0.1M Bis-Tris pH 6.5
Matthews coefficient: 2.92
Solvent content (%): 57.85
Release date: 2021-10-13
Structure of Cyclophilin A in complex with GlyPro. (PDB entry 4N1M)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 168 residues
Sequence: SHMMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.15
R work: 0.13376
R free: 0.16337
Average B factor: 9.017
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: Tris, PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2.6
Solvent content (%): 52.66
Ligand: GLYCINE (GLY)
Ligand formula: C2 H5 N O2
Ligand molecular weight: 75.067
Ligand SMILES: C(C(=O)O)N
Ligand InChI: InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
Release date: 2015-08-12