satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of Protein Lysine Methyltransferase SMYD2 in complex with LLY-507, a Cell-Active, Potent and Selective Inhibitor (PDB entry 4WUY)
Macromolecule: N-lysine methyltransferase SMYD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 441 residues
Sequence: MRAEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIESHEGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.15116
R free: 0.20013
Average B factor: 23.395
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 281
Crystal growth procedure: 100 mM Tris HCl pH 8.6, 14% PEG 20K and 200 mM Sodium Chloride
Matthews coefficient: 2.64
Solvent content (%): 53.42
Ligand: 5-cyano-2'-{4-[2-(3-methyl-1H-indol-1-yl)ethyl]piperazin-1-yl}-N-[3-(pyrrolidin-1-yl)propyl]biphenyl-3-carboxamide (3UJ)
Ligand formula: C36 H42 N6 O
Ligand molecular weight: 574.758
Ligand SMILES: Cc1cn(c2c1cccc2)CCN3CCN(CC3)c4ccccc4c5cc(cc(c5)C(=O)NCCCN6CCCC6)C#N
Ligand InChI: InChI=1S/C36H42N6O/c1-28-27-42(34-11-4-2-9-32(28)34)22-19-40-17-20-41(21-18-40)35-12-5-3-10-33(35)30-23-29(26-37)24-31(25-30)36(43)38-13-8-16-39-14-6-7-15-39/h2-5,9-12,23-25,27H,6-8,13-22H2,1H3,(H,38,43)
Release date: 2015-04-08
Crystal structure of a human calcium/calmodulin dependent serine protein kinase (CASK) PDZ domain in complex with Neurexin-1 peptide (PDB entry 6NID)
Macromolecule: Peripheral plasma membrane protein CASK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 88 residues
Sequence: MGRVRLVQFQKNTDEPMGITLKMNELNHCIVARIMHGGMIHRQGTLHVGDEIREINGISVANQTVEQLQKMLREMRGSITFKIVPSYR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1918
R free: 0.2396
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.01M tri-sodium citrate
33% (w/v) PEG 6000
Matthews coefficient: 1.94
Solvent content (%): 36.73
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: 2020-01-01
Crystal structure of TRIM24 PHD-bromodomain complexed with N-[6-(4-methoxyphenoxy)-1,3-dimethyl-2-oxo-2,3-dihydro-1H-1,3-benzodiazol-5-yl]benzenesulfonamide (5g) (PDB entry 4YAX)
Macromolecule: Transcription intermediary factor 1-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 184 residues
Sequence: SPNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPSHNSEKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.17
R free: 0.235
Average B factor: 26.67
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 2.2-2.4M ammonium sulfate, 0.1M HEPES buffer pH 7.5, 2% PEG400 and 8-9% glycerol
Matthews coefficient: 2.35
Solvent content (%): 47.74
Ligand: N-[6-(4-methoxyphenoxy)-1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl]benzenesulfonamide (4AE)
Ligand formula: C22 H21 N3 O5 S
Ligand molecular weight: 439.484
Ligand SMILES: CN1c2cc(c(cc2N(C1=O)C)Oc3ccc(cc3)OC)NS(=O)(=O)c4ccccc4
Ligand InChI: InChI=1S/C22H21N3O5S/c1-24-19-13-18(23-31(27,28)17-7-5-4-6-8-17)21(14-20(19)25(2)22(24)26)30-16-11-9-15(29-3)10-12-16/h4-14,23H,1-3H3
Release date: 2015-06-24
Structure of NVP-AEW541 in complex with IGF-1R kinase (PDB entry 5HZN)
Macromolecule: Insulin-like growth factor 1 receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 304 residues
Sequence: AADVYVPDEWEVAREKITMSRELGQGSFGMVYEGVAKGVVKDEPETRVAIKTVNEAASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQGQPTLVIMELMTRGDLKSYLRSLRPAMANNPVLAPPSLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGMTRDIYETDYYRKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSNEQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEMEPGFREVSFYYSEENK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.194
R free: 0.2178
Average B factor: 45.611
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.25
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG8000, 0.1M MES PH6.25, 0.2 M AMMONIUM SULFATE, 4% GLYCEROL
Matthews coefficient: 2.97
Solvent content (%): 58.63
Ligand: 7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine (66A)
Ligand formula: C27 H29 N5 O
Ligand molecular weight: 439.552
Ligand SMILES: c1ccc(cc1)COc2cccc(c2)c3cn(c4c3c(ncn4)N)C5CC(C5)CN6CCC6
Ligand InChI: InChI=1S/C27H29N5O/c28-26-25-24(21-8-4-9-23(14-21)33-17-19-6-2-1-3-7-19)16-32(27(25)30-18-29-26)22-12-20(13-22)15-31-10-5-11-31/h1-4,6-9,14,16,18,20,22H,5,10-13,15,17H2,(H2,28,29,30)/t20-,22+
Release date: 2016-04-06
Crystal structure of the catalytic fragment of masp-1 in complex with SFMI1 (PDB entry 7ARX)
Macromolecule: Mannan-binding lectin serine protease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 155 residues
Sequence: ASMTGNECPELQPPVHGKIEPSQAKYFFKDQVLVSCDTGYKVLKDNVEMDTFQIECLKDGTWSNKIPTCKIVDCRAPGELEHGLITFSTRNNLTTYKSEIKYSCQEPYYKMLNNNTGIYTCSAQGVWMNKVLGRSLPTCLPVCGLPKFSRKLMAR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.42
R work: 0.256
R free: 0.2849
Average B factor: 76.57
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Hepes, 42 w/v% PEG200, pH 7.5
Matthews coefficient: 2.39
Solvent content (%): 48.45
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2021-11-03
CRYSTAL STRUCTURE of PPC2A-D38K (PDB entry 4RAG)
Macromolecule: Protein phosphatase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 367 residues
Sequence: GAFLDKPKMEKHNAQGQGNGLRYGLSSMQGWRVEMEKAHTAVIGLPSGLESWSFFAVYDGHAGSQVAKYCCEHLLDHITNNQDFKGSAGAPSVENVKNGIRTGFLEIDEHMRVMSEKKHGADRSGSTAVGVLISPQHTYFINCGDSRGLLCRNRKVHFFTQDHKPSNPLEKERIQNAGGSVMIQRVNGSLAVSRALGDFDYKCVHGKGPTEQLVSPEPEVHDIERSEEDDQFIILACDGIWDVMGNEELCDFVRSRLEVTDDLEKVCNEVVDTCLYKGSRDNMSVILICFPNAPKVSPEAVKKEAELDKYLECRVEEIIKKQGEGVPDLVHVMRTLASENIPSLPPGGELASKRNVIEAVYNRLNPY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1991
R free: 0.2297
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 15%(v/v) PEG8000, pH 5.5, 50mM K2HPO4, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Matthews coefficient: 3.08
Solvent content (%): 60.03
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2015-08-26
Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 80 s (PDB entry 4RQ0)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 343 residues
Sequence: MGMSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.20751
R free: 0.26822
Average B factor: 27.769
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Matthews coefficient: 2.14
Solvent content (%): 42.46
Ligand: PYROPHOSPHATE (PPV)
Ligand formula: H4 O7 P2
Ligand molecular weight: 177.975
Ligand SMILES: OP(=O)(O)OP(=O)(O)O
Ligand InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)
Release date: 2015-04-15
ERK2 covelently bound to RU76 cyclohexenone based inhibitor (PDB entry 8PT1)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 364 residues
Sequence: GSASMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1791
R free: 0.2064
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG8000, 0.1 M HEPES pH 7.5
Matthews coefficient: 2.42
Solvent content (%): 49.3
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: 2024-07-24
Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (4-oxoquinazolin-3(4H)-yl)acetic acid (PDB entry 6NFT)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 121 residues
Sequence: GGEVRQVSKHAFSLKQLDNPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNNHAVEHYRETGYPLAVKLGTITPDGADVYSYDEDDMVLDPSLAEHLSHFGIDMLKMQKTD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1802
R free: 0.2062
Average B factor: 17.248
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 2 M sodium/potassium phosphate pH 7.0, 1.1% DMSO (v/v), 25% ethylene glycol (v/v)
Matthews coefficient: 2.87
Solvent content (%): 57.17
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: 2019-01-02
aSMase with zinc and phosphocholine (PDB entry 5I85)
Macromolecule: Sphingomyelin phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.12
Sequence length: 583 residues
Sequence: LSDSRVLWAPAEAHPLSPQGHPARLHRIVPRLRDVFGWGNLTCPICKGLFTAINLGLKKEPNVARVGSVAIKLCNLLKIAPPAVCQSIVHLFEDDMVEVWRRSVLSPSEACGLLLGSTCGHWDIFSSWNISLPTVPKPPPKPPSPPAPGAPVSRILFLTDLHWDHDYLEGTDPDCADPLCCRRGSGLPPASRPGAGYWGEYSKCDLPLRTLESLLSGLGPAGPFDMVYWTGDIPAHDVWHQTRQDQLRALTTVTALVRKFLGPVPVYPAVGNHESTPVNSFPPPFIEGNHSSRWLYEAMAKAWEPWLPAEALRTLRIGGFYALSPYPGLRLISLNMNFCSRENFWLLINSTDPAGQLQWLVGELQAAEDRGDKVHIIGHIPPGHCLKSWSWNYYRIVARYENTLAAQFFGHTHVDEFEVFYDEETLSRPLAVAFLAPSATTYIGLNPGYRVYQIDGNYSGSSHVVLDHETYILNLTQANIPGAIPHWQLLYRARETYGLPNTLPTAWHNLVYRMRGDMQLFQTFWFLYHKGHPPSEPCGTPCRLATLCAQLSARADSPALCRHLMPDGSLPEAQSLWPRPLFC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1903
R free: 0.2218
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: phosphocholine soaked in well solution containing 1.5 M ammonium sulfate, 0.1 M sodium acetate pH 5.0-5.5, 12% glycerol.
Matthews coefficient: 3.62
Solvent content (%): 66.02
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: 2016-09-07
TGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D,I211V,Y249F, S280T,Y282F,S287N,A350C,L352F) IN COMPLEX WITH 3-AMINO-6- [4-(2-HYDROXYETHYL)PHENYL]-N-[4-(MORPHOLIN-4-YL)PYRIDIN-3-YL]PYRAZINE-2-CARBOXAMIDE (PDB entry 5E90)
Macromolecule: TGF-beta receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 307 residues
Sequence: GHMTIARDIVLQESVGKGRFGEVWRGKWRGEEVAVKIFSSREERSWFREAEIFQTVMLRHENILGFIAADNKDNGTWTQLWLVTDFHEHGNLFDYLNRYTVTVEGMIKLALSTASGLAHLHMEIVGTQGKPAIAHRDLKSKNILVKKNGTCCICDFGLAVRHDSATDTIDIAPNHRVGTKRYMAPEVLDDSINMKHFESFKRADIYAMGLVFWEIARRCSIGGIHEDYQLPYYDLVPSDPSVEEMRKVVCEQKLRPNIPNRWQSCEALRVMAKIMRECWYANGAARLTALRIKKTLSQLSQQEGIKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1756
R free: 0.2179
Average B factor: 27.39
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 277
Crystal growth procedure: 23%(w/v) PEG3350, 3%(v/v) glcyerol
Matthews coefficient: 2.1
Solvent content (%): 41.42
Ligand: 3-amino-6-[4-(2-hydroxyethyl)phenyl]-N-[4-(morpholin-4-yl)pyridin-3-yl]pyrazine-2-carboxamide (5L4)
Ligand formula: C22 H24 N6 O3
Ligand molecular weight: 420.464
Ligand SMILES: c1cc(ccc1CCO)c2cnc(c(n2)C(=O)Nc3cnccc3N4CCOCC4)N
Ligand InChI: InChI=1S/C22H24N6O3/c23-21-20(26-17(14-25-21)16-3-1-15(2-4-16)6-10-29)22(30)27-18-13-24-7-5-19(18)28-8-11-31-12-9-28/h1-5,7,13-14,29H,6,8-12H2,(H2,23,25)(H,27,30)
Release date: 2016-05-11
FKBP51FK1 F67E/K60Orn (i, i+7) in complex with SAFit1 (PDB entry 8PJ8)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPLIGDKVYVHYKGALSNGKKEDSSHDRNEPFVFSLGKGQVIKAWDIGVATLKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1838
R free: 0.2069
Average B factor: 24.414
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG3350, 0.2M NH4-acetate, 0.1M HEPES-NaOH pH 7.5
Matthews coefficient: 2.24
Solvent content (%): 45.2
Ligand: 2-[3-[(1~{R})-1-[(2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidin-2-yl]carbonyloxy-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid (GY1)
Ligand formula: C42 H53 N O11
Ligand molecular weight: 747.87
Ligand SMILES: COc1ccc(cc1OC)CCC(c2cccc(c2)OCC(=O)O)OC(=O)C3CCCCN3C(=O)C(c4cc(c(c(c4)OC)OC)OC)C5CCCCC5
Ligand InChI: InChI=1S/C42H53NO11/c1-48-34-20-18-27(22-35(34)49-2)17-19-33(29-14-11-15-31(23-29)53-26-38(44)45)54-42(47)32-16-9-10-21-43(32)41(46)39(28-12-7-6-8-13-28)30-24-36(50-3)40(52-5)37(25-30)51-4/h11,14-15,18,20,22-25,28,32-33,39H,6-10,12-13,16-17,19,21,26H2,1-5H3,(H,44,45)/t32-,33+,39-/m0/s1
Release date: 2024-03-06
Ca2+-Calmodulin in complex with peptide from brain-type creatine kinase in extended 1:2 binding mode (PDB entry 7BF1)
Macromolecule: Calmodulin-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 149 residues
Sequence: MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.24
R work: 0.1351
R free: 0.1863
Average B factor: 23.434
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 1500, 0.1 M SPG buffer pH 4-5. 
CaM-CKBpeptide ratios of 1:4
Matthews coefficient: 1.77
Solvent content (%): 30.7
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: 2021-07-21
Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable CTP and MANGANESE (PDB entry 6CU9)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.1937
R free: 0.2408
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.24
Solvent content (%): 45.15
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2019-03-27
DeltaC3 C-terminal truncation of HsNMT1 in complex with MyrCoA and GDCFSKPR substrates (PDB entry 6SK8)
Macromolecule: Glycylpeptide N-tetradecanoyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.97
Sequence length: 399 residues
Sequence: GGSEFSVGQGPAKTMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.2078
R free: 0.2439
Average B factor: 30.2305
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 19% PEG8K, 100mM Sodium Citrate pH 5.6, 100mM MgCl2, 100mM NaCl
Matthews coefficient: 2.22
Solvent content (%): 44.57
Ligand: TETRADECANOYL-COA (MYA)
Ligand formula: C35 H62 N7 O17 P3 S
Ligand molecular weight: 977.89
Ligand SMILES: CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C35H62N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-26(44)63-19-18-37-25(43)16-17-38-33(47)30(46)35(2,3)21-56-62(53,54)59-61(51,52)55-20-24-29(58-60(48,49)50)28(45)34(57-24)42-23-41-27-31(36)39-22-40-32(27)42/h22-24,28-30,34,45-46H,4-21H2,1-3H3,(H,37,43)(H,38,47)(H,51,52)(H,53,54)(H2,36,39,40)(H2,48,49,50)/t24-,28-,29-,30+,34-/m1/s1
Release date: 2020-03-18
Crystal structure of XIAP-BIR2 domain complexed with (S)-3-(4-methoxyphenyl)-2-((S)-2-((S)-1-((S)-2-((S)-2-(methylamino)propanamido)pent-4-ynoyl)pyrrolidine-2-carboxamido)-3-phenylpropanamido)propanoic acid (PDB entry 4WVS)
Macromolecule: E3 ubiquitin-protein ligase XIAP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 98 residues
Sequence: MGSSHHHHHHSSGETVRFQGHMRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGDQVQCFACGGKLKNWEPGDRAWSEHRRHFPNCFFVL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.1636
R free: 0.2316
Average B factor: 21.88
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystals were grown in 0.98 M Ammonium Sulfate and 0.1 M Ammonium Formate. Single crystals grew after streak seeding
Matthews coefficient: 1.68
Solvent content (%): 29.01
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: 2015-05-06
Tandem Tudor and PHD domains of UHRF2 (PDB entry 4TVR)
Macromolecule: E3 ubiquitin-protein ligase UHRF2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 280 residues
Sequence: GNQPSTSARARLIDPGFGIYKVNELVDARDVGLGAWFEAHIHSVTRASDGQSRGKTPLKNGNIKHKSKENTNKLDSVPSTSNSDCVAADEDVIYHIQYDEYPESGTLEMNVKDLRPRARTILKWNELNVGDVVMVNYNVESPGQRGFWFDAEITTLKTISRTKKELRVKIFLGGSEGTLNDCKIISVDEIFKIERPGAHPLSFADGKFLRRNDPECDLCGGDPEKKCHSCSCRVCGGKHEPNMQLLCDECNVAYHIYCLNPPLDKVPAEEYWYCPSCKTD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29
R work: 0.22902
R free: 0.25982
Average B factor: 81.091
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG-3350, 0.2 M
NaCl, 0.1 M HEPES pH 7.5, 5% glycerol
Matthews coefficient: 2.43
Solvent content (%): 49.41
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: 2015-06-24
Crystal structure of CDK2 in complex with 6-chloro-7H-purine processed with the CrystalDirect automated mounting and cryo-cooling technology (PDB entry 5ANI)
Macromolecule: CYCLIN-DEPENDENT KINASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.18767
R free: 0.23258
Average B factor: 41.111
Crystal growth procedure: 0.02 M HEPES, PH=7.0, 5% GLYCEROL, 12% PEG 3350
Matthews coefficient: 2.01
Solvent content (%): 38.78
Ligand: 6-chloro-9H-purine (ES4)
Ligand formula: C5 H3 Cl N4
Ligand molecular weight: 154.557
Ligand SMILES: c1[nH]c2c(n1)c(ncn2)Cl
Ligand InChI: InChI=1S/C5H3ClN4/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H,7,8,9,10)
Release date: 2016-04-13
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z296300542 (PDB entry 5QOU)
Macromolecule: DCP2 (NUDT20)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.62
Sequence length: 167 residues
Sequence: SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLARLYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGFSSTGSTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.19
R work: 0.1946
R free: 0.2516
Average B factor: 53.753
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M acetate, pH 4.5, 5-25% PEG3350
Matthews coefficient: 2.51
Solvent content (%): 51.04
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: 2019-05-08