satarupa22/MacromolecularLigandDB huggingface dataset:
Human PPARgamma ligand-binding domain R288A mutant in complex with imatinib (PDB entry 6KTN)
Macromolecule: Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 283 residues
Sequence: AEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFASVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.752
R work: 0.2205
R free: 0.2563
Average B factor: 44.711
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 296
Crystal growth procedure: 2.2 M sodium malonate (pH 7.0)
Matthews coefficient: 2.7
Solvent content (%): 54.5
Ligand: 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE (STI)
Ligand formula: C29 H31 N7 O
Ligand molecular weight: 493.603
Ligand SMILES: Cc1ccc(cc1Nc2nccc(n2)c3cccnc3)NC(=O)c4ccc(cc4)CN5CCN(CC5)C
Ligand InChI: InChI=1S/C29H31N7O/c1-21-5-10-25(18-27(21)34-29-31-13-11-26(33-29)24-4-3-12-30-19-24)32-28(37)23-8-6-22(7-9-23)20-36-16-14-35(2)15-17-36/h3-13,18-19H,14-17,20H2,1-2H3,(H,32,37)(H,31,33,34)
Release date: 2020-02-05
Crystal structure of EGFR_DMX in complex with compound 7 (PDB entry 8HV5)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.18577
R free: 0.22445
Average B factor: 57.309
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1M TRIS pH 8.5, 0.15M Sodium citrate, 25%PEG400
Matthews coefficient: 3.36
Solvent content (%): 63.4
Ligand: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL (PE5)
Ligand formula: C18 H38 O9
Ligand molecular weight: 398.489
Ligand SMILES: CCOCCOCCOCCOCCOCCOCCOCCOCCO
Ligand InChI: InChI=1S/C18H38O9/c1-2-20-5-6-22-9-10-24-13-14-26-17-18-27-16-15-25-12-11-23-8-7-21-4-3-19/h19H,2-18H2,1H3
Release date: 2023-12-13
Crystal structure of Apo-form LMW-PTP (PDB entry 5KQP)
Macromolecule: Low molecular weight phosphotyrosine protein phosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 178 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMAEQATKSVLFVCLGNICRSPIAEAVFRKLVTDQNISENWRVDSAATSGYEIGNPPDYRGQSCMKRHGIPMSHVARQITKEDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSDFETVYQQCVRCCRAFLEKAH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.052
R work: 0.1931
R free: 0.2663
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: Crystals grew under the following condition: 30% PEGME 5000, 0.2 M ammonium sulfate, 100 mM MES buffer, pH=6.5. Then crystal were transferred to buffer containing 30% PEGME 5000, 0.2 M ammonium sulfate, 100 mM Bis-Tris, pH=6.5 to deplete the bound MES.
Matthews coefficient: 2.11
Solvent content (%): 41.67
Release date: 2016-10-12
Crystal structure of a PMS2 variant (PDB entry 6MFQ)
Macromolecule: Mismatch repair endonuclease PMS2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 369 residues
Sequence: GSHMMERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTRLMFDHNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKEFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNQLEQGKRQPVVCTGGSPSIKENIGSVFGQKQLQSLIPFVQLPPSDSVCEEYGLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINRRPCDPAKVCRLVNEVYHMYNRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSLIGMFDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2214
R free: 0.2316
Average B factor: 50.2596
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 289.15
Crystal growth procedure: Crystals were obtained in conditions containing 4% tacsimate pH 5 (v/v) and 25% PEG 3350 (w/v). The concentrated PMS2 G207E protein (7 mg/mL) was combined with 0.1ul of an additive (0.1 M calcium chloride dehydrate) prior to the addition of crystallization reagent in a 1:1 ratio.
Matthews coefficient: 2.33
Solvent content (%): 47.14
Release date: 2019-02-06
X-Ray structure of human Serine/Threonine Kinase 17B (STK17B) aka DRAK2 in complex with ADP obtained by on-chip soaking (PDB entry 6QF4)
Macromolecule: Serine/threonine-protein kinase 17B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 327 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMENFNNFYILTSKELGRGKFAVVRQCISKSTGQEYAAKFLKKRRRGQDCRAEILHEIAVLELAKSCPRVINLHEVYENTSEIILILEYAAGGEIFSLCLPELAEMVSENDVIRLIKQILEGVYYLHQNNIVHLDLKPQNILLSSIYPLGDIKIVDFGMSRKIGHACELREIMGTPEYLAPEILNYDPITTATDMWNIGIIAYMLLTHTSPFVGEDNQETYLNISQVNVDYSEETFSSVSQLATDFIQSLLVKNPEKRPTAEICLSHSWLQQWDFENLFHPEETSSSSQTQDHSVRSSEDKTSKSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.495
R work: 0.1827
R free: 0.2268
Average B factor: 57.04
Crystallization method: BATCH MODE
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.2M ammonium acetate, 20% PEG 3350, 50mM sodium/potassium tartrate, 0.8mM quercetin
Matthews coefficient: 2.89
Solvent content (%): 57.43
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2019-07-10
Crystal structure of a superbinder Src SH2 domain (sSrcF) in complex with a high affinity phosphopeptide (PDB entry 7T1U)
Macromolecule: Proto-oncogene tyrosine-protein kinase Src
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 111 residues
Sequence: GGAPWQAEEWYFGKITRRESERLLLNAENPRGTFLVREGQSQPDYVLSVSDFDNAKGLNVKHYIIRKLDSGGFYITSRTQFNSLQQLVAYYSKHADGLCHRLTTVCPTSRA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2184
R free: 0.2702
Average B factor: 56.06
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 293
Crystal growth procedure: 80 uM Zinc Acetate, 12% PEG3350, 100 mM Sodium Acetate (pH 4.0), and 2% 1,3-butanediol
Matthews coefficient: 2.13
Solvent content (%): 42.38
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: 2022-08-24
Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dATP soaked with MgCl2 for 80 s (PDB entry 4RQ6)
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): 2.25
R work: 0.19766
R free: 0.25204
Average B factor: 44.391
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: 2.19
Solvent content (%): 43.89
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
Structure of Casein kinase I isoform delta (CK1d) complexed with inhibitor 15 (PDB entry 8VXF)
Macromolecule: Casein kinase I isoform delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 300 residues
Sequence: GMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLKFGASR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.2255
R free: 0.2707
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 12%-20% PEG 10 K, 0.1 M Bis Tris (pH 5.5), 0.1 M Ammonium Acetate
Matthews coefficient: 2.39
Solvent content (%): 48.59
Ligand: (2P,3P,8S)-2-(5-fluoropyridin-2-yl)-6,6-dimethyl-3-(1H-pyrazolo[3,4-b]pyridin-4-yl)-6,7-dihydro-4H-pyrazolo[5,1-c][1,4]oxazine (A1AD8)
Ligand formula: C19 H17 F N6 O
Ligand molecular weight: 364.376
Ligand SMILES: CC1(Cn2c(c(c(n2)c3ccc(cn3)F)c4ccnc5c4cn[nH]5)CO1)C
Ligand InChI: InChI=1S/C19H17FN6O/c1-19(2)10-26-15(9-27-19)16(12-5-6-21-18-13(12)8-23-24-18)17(25-26)14-4-3-11(20)7-22-14/h3-8H,9-10H2,1-2H3,(H,21,23,24)
Release date: 2024-05-08
Crystal structure of Dot1L in complex with inhibitor CPD2 [2-(2-(5-((2-chlorophenoxy)methyl)-1H-tetrazol-1-yl)acetyl)-N-(4-chlorophenyl)hydrazinecarboxamide] (PDB entry 5DRT)
Macromolecule: Histone-lysine N-methyltransferase, H3 lysine-79 specific
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 334 residues
Sequence: GPGEKLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKNPG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.69
R work: 0.1751
R free: 0.1967
Average B factor: 61.97
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 1.3M K/Na tartrate
0.1M Hepes pH7.2
Matthews coefficient: 3.48
Solvent content (%): 64.67
Ligand: 2-({5-[(2-chlorophenoxy)methyl]-1H-tetrazol-1-yl}acetyl)-N-(4-chlorophenyl)hydrazinecarboxamide (5EG)
Ligand formula: C17 H15 Cl2 N7 O3
Ligand molecular weight: 436.252
Ligand SMILES: c1ccc(c(c1)OCc2nnnn2CC(=O)NNC(=O)Nc3ccc(cc3)Cl)Cl
Ligand InChI: InChI=1S/C17H15Cl2N7O3/c18-11-5-7-12(8-6-11)20-17(28)23-22-16(27)9-26-15(21-24-25-26)10-29-14-4-2-1-3-13(14)19/h1-8H,9-10H2,(H,22,27)(H2,20,23,28)
Release date: 2016-06-15
Crystal Structure of human cyclic GMP-AMP synthase in complex with 2-[(2-chlorophenyl)methylamino]-5-[(2-fluoroanilino)methyl]-4H-[1,2,4]triazolo[1,5-a]pyrimidin-7-one (PDB entry 7FUO)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.1968
R free: 0.2592
Average B factor: 61.8423
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals.
Matthews coefficient: 2.66
Solvent content (%): 53.78
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2024-02-21
Crystal Structure of human Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase (PDB entry 7W8B)
Macromolecule: Isoform 5 of Focal adhesion kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 164 residues
Sequence: SSPADSYNEGVKPWRLQPQEISPPPTANLDRSNDKVYENVTGLVKAVIEMSSKIQPAPPEEYVPMVKEVGLALRTLLATVDETIPLLPASTHREIEMAQKLLNSDLGELINKMKLAQQYVMTSLQQEYKKQMLTAAHALAVDAKNLLDVIDQARLKMLGQTRPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.093
R work: 0.2395
R free: 0.2862
Average B factor: 63.82
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 2500 mM Sodium chloride 100 mM Imidazole/ Hydrochloric acid pH 8.0
Matthews coefficient: 2.18
Solvent content (%): 43.55
Release date: 2023-07-05
Human Exonuclease 5 crystal structure (PDB entry 7LW7)
Macromolecule: Exonuclease V
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 346 residues
Sequence: SNALEDAQESKALVNMPGPSSESLGKDDKPISLQNWKRGLDILSPMERFHLKYLYVTDLATQNWCELQTAYGKELPGFLAPEKAAVLDTGASIHLARELELHDLVTVPVTTKEDAWAIKFLNILLLIPTLQSEGHIREFPVFGEVEGVLLVGVIDELHYTAKGELELAELKTRRRPMLPLEAQKKKDCFQVSLYKYIFDAMVQGKVTPASLIHHTKLCLEKPLGPSVLRHAQQGGFSVKSLGDLMELVFLSLTLSDLPVIDILKIEYIHQETATVLGTEIVAFKEKEVRAKVQHYMAYWMGHREPQGVDVEEAWKCRTCTYADICEWRKGSGVLSSTLAPQVKKAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1821
R free: 0.2245
Average B factor: 41.6189
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350 and 0.2 M lithium acetate
Matthews coefficient: 2.63
Solvent content (%): 53.24
Ligand: IRON/SULFUR CLUSTER (SF4)
Ligand formula: Fe4 S4
Ligand molecular weight: 351.64
Ligand SMILES: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
Ligand InChI: InChI=1S/4Fe.4S
Release date: 2021-07-14
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000383a (PDB entry 7GSE)
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): 1.89
R work: 0.1993
R free: 0.2348
Average B factor: 41.778
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.33
Solvent content (%): 63.1
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
Human MOF K274P crystal structure (PDB entry 5J8F)
Macromolecule: Histone acetyltransferase KAT8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 307 residues
Sequence: MGSSHHHHHHDYDIPTTENLYFQGSKYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPPGKEIYRKSNISVYEVDGKDHKIYCQNLCLLAKLFLDHPTLYFDVEPFVFYILTEVDRQGAHIVGYFSKEKESPDGNNVACILTLPPYQRRGYGKFLIAFSYELSKLESTVGSPEKPLSDLGKLSYRSYWSWVLLEILRDFRGTLSIKDLSQMTSITQNDIISTLQSLNMVKYWKGQHVICVTPKLVEEHLKSAQYKKPPITVDSVCLKWAPPKHKQVKLSKK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2391
R free: 0.2757
Average B factor: 41.09
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.28M Ammonium Chloride
26%PEG 3350
0.1M BisTris-HCl pH 6.5
Matthews coefficient: 2.19
Solvent content (%): 43.77
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: 2016-07-20
Discovery of a Potent Cyclophilin Inhibitor (Compound 6) based on Structural Simplification of Sanglifehrin A (PDB entry 5T9Z)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 163 residues
Sequence: VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1628
R free: 0.1901
Average B factor: 15.126
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 4.2
Crystallization temperature (K): 293
Crystal growth procedure: sodium citrate, pH 4.2
25% (w/v) PEG 3350
Matthews coefficient: 2.17
Solvent content (%): 43.19
Ligand: 11-[(3-hydroxyphenyl)methyl]-18-methoxy-17-methyl-14-(propan-2-yl)-3-oxa-9,12,15,28-tetraazatricyclo[21.3.1.1~5,9~]octacosa-1(27),21,23,25-tetraene-4,10,13,16-tetrone (78R)
Ligand formula: C35 H46 N4 O7
Ligand molecular weight: 634.762
Ligand SMILES: CC1C(CCC=Cc2cccc(c2)COC(=O)C3CCCN(N3)C(=O)C(NC(=O)C(NC1=O)C(C)C)Cc4cccc(c4)O)OC
Ligand InChI: InChI=1S/C35H46N4O7/c1-22(2)31-33(42)36-29(20-25-12-8-14-27(40)19-25)34(43)39-17-9-15-28(38-39)35(44)46-21-26-13-7-11-24(18-26)10-5-6-16-30(45-4)23(3)32(41)37-31/h5,7-8,10-14,18-19,22-23,28-31,38,40H,6,9,15-17,20-21H2,1-4H3,(H,36,42)(H,37,41)/b10-5+/t23-,28+,29+,30-,31+/m1/s1
Release date: 2017-01-25
ALK2 antibody complex (PDB entry 7YRU)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 109 residues
Sequence: MEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPGTQNFHLEHHHHHH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2453
R free: 0.2708
Average B factor: 49.498
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 298
Crystal growth procedure: 2% Tacsimate pH 7.0, 0.1 M HEPES pH 7.5, 20% PEG 3350
Matthews coefficient: 2.21
Solvent content (%): 44.41
Release date: 2023-05-17
Crystal structure of PKAc-PLN complex (PDB entry 7E0Z)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 2.7.11.11
Sequence length: 358 residues
Sequence: SNAMGNAAAAKKGSEQESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEFIGSG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.162
R work: 0.179
R free: 0.2276
Average B factor: 30.8797
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298.15
Crystal growth procedure: 0.1M Bis-Tris, pH 6.5, 25% PEG 3350
Matthews coefficient: 2.14
Solvent content (%): 42.6
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: 2022-04-27
Crystal Structure of MavC in Complex with Ub-UbE2N (PDB entry 6P5B)
Macromolecule: MavC
Type: Protein, polypeptide(L)
Source organism: Legionella pneumophila
Sequence length: 389 residues
Sequence: GPLGSMTTSKLEKTGLHVHEKIKHMVKNYGTMITGIPAEILGQNEAEISVGYVKKMGNMKENIAEVVRKSEMTQPTNSAGKASNEVCDLLLGTEGASEFEKSSYQVLSGDGSNLKGSLPNKNLLVRVEMDRFNAPQKYQKIKREEFNPETAEKNKIYLLEDQLVYLDIFGKVIDLGQTSDTCHRLFNAITTPFYQNYILYDEYIDPEESAEEAAMFEMGEIVKAKMKNIDCWTATHSFTIFVPESDSEDTRTLYPYQAYWTSHTLQQWFSGDKDEKLSRLGIDGYIEKLALLGTTTDSKIRSSIYGELFSPPGKEHVFCTGMNEKFSPLRVKFKVTEVNPEIALQNLEEVQEFIDTNYPGENAKDQCELYKIKAQEAMTKQLEMRLLIE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.099
R work: 0.1949
R free: 0.2319
Average B factor: 37.4283
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 298
Crystal growth procedure: 0.2 M Na Malonate, 25% PEG 3350, 10 mM NiCl2
Matthews coefficient: 2.4
Solvent content (%): 48.82
Release date: 2020-05-27
TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea (PDB entry 5KMN)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 330 residues
Sequence: XSSLSPTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.1936
R free: 0.2223
Average B factor: 37.66
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside
Matthews coefficient: 2.41
Solvent content (%): 48.93
Ligand: 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea (6UK)
Ligand formula: C20 H17 F3 N4 O
Ligand molecular weight: 386.37
Ligand SMILES: Cc1ncc(c(n1)c2ccccc2)NC(=O)NCc3ccccc3C(F)(F)F
Ligand InChI: InChI=1S/C20H17F3N4O/c1-13-24-12-17(18(26-13)14-7-3-2-4-8-14)27-19(28)25-11-15-9-5-6-10-16(15)20(21,22)23/h2-10,12H,11H2,1H3,(H2,25,27,28)
Release date: 2016-12-28