satarupa22/MacromolecularLigandDB huggingface dataset:
The tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM peptide (PDB entry 7Q5W)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 265 residues
Sequence: SMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRNYLGGFALSVAHGRKAHHYTIERELNGTYAIAGGRTHASPADLCHYHSQESDGLVCLLKKPFNRPQGVQPKTGPFEDLKENLIREYVKQTWNLQGQALEQAIISQKPQLEKLIATTAHEKMPWFHGKISREESEQIVLIGSKTNGKFLIRARDNNGSYALCLLHEGKVLHYRIDKDKTGKLSIPEGKKFDTLWQLVEHYSYKADGLLRVLTVPCQKIGTQGNVN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2336
R free: 0.2663
Average B factor: 61.064
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM Tris/BICINE, 10% PEG 20,000, 20% PEG 500 MME
Matthews coefficient: 2.93
Solvent content (%): 58.01
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: 2021-11-24
MYST histone acetyltransferase KAT6A/B in complex with WM-1119 (PDB entry 6CT2)
Macromolecule: Histone acetyltransferase KAT8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 295 residues
Sequence: MGSSHHHHHHSSGLVPRGSTKVKYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPPGKEIYRKSNISVHEVDGKDHKIYCQNLCLLAKLFLDHKTLYFDVEPFVFYILTEVDRQGAHIVGYFSKEKESPDGNNVSCIMILPPYQRRGYGRFLIAFSYELSKLESTVGSPEKPLSDLGKLSYRSYWSWVLLENLRDFRGTLSIKDLSQMTSITQNDIISTLQSLNMVKYWKGQHVICVTPKLVEEHLKSAQYKKPPITVDSVCLKWAPPK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.128
R work: 0.2005
R free: 0.2355
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 0.196 M MgCl2, 19.5 % PEG 3350, and 0.1 M bis-tris chloride at pH 5.5
Matthews coefficient: 2.25
Solvent content (%): 45.4
Ligand: 3-fluoro-N'-[(2-fluorophenyl)sulfonyl]-5-(pyridin-2-yl)benzohydrazide (FCV)
Ligand formula: C18 H13 F2 N3 O3 S
Ligand molecular weight: 389.376
Ligand SMILES: c1ccc(c(c1)F)S(=O)(=O)NNC(=O)c2cc(cc(c2)F)c3ccccn3
Ligand InChI: InChI=1S/C18H13F2N3O3S/c19-14-10-12(16-6-3-4-8-21-16)9-13(11-14)18(24)22-23-27(25,26)17-7-2-1-5-15(17)20/h1-11,23H,(H,22,24)
Release date: 2018-08-01
FXIIIa in complex with the inhibitor Mi0621 (PDB entry 5MHL)
Macromolecule: Coagulation factor XIII A chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.13
Sequence length: 738 residues
Sequence: MHHHHHHSETSRTAFGGRRAVPPNNSNAAEDDLPTVELQGVVPRGVNLQEFLNVTSVHLFKERWDTNKVDHHTDKYENNKLIVRRGQSFYVQIDFSRPYDPRRDLFRVEYVIGRYPQENKGTYIPVPIVSELQSGKWGAKIVMREDRSVRLSIQSSPKCIVGKFRMYVAVWTPYGVLRTSRNPETDTYILFNPWCEDDAVYLDNEKEREEYVLNDIGVIFYGEVNDIKTRSWSYGQFEDGILDTCLYVMDRAQMDLSGRGNPIKVSRVGSAMVNAKDDEGVLVGSWDNIYAYGVPPSAWTGSVDILLEYRSSENPVRYGQCWVFAGVFNTFLRCLGIPARIVTNYFSAHDNDANLQMDIFLEEDGNVNSKLTKDSVWNYHCWNEAWMTRPDLPVGFGGWQAVDSTPQENSDGMYRCGPASVQAIKHGHVCFQFDAPFVFAEVNSDLIYITAKKDGTHVVENVDATHIGKLIVTKQIGGDGMMDITDTYKFQEGQEEERLALETALMYGAKKPLNTEGVMKSRSNVDMDFEVENAVLGKDFKLSITFRNNSHNRYTITAYLSANITFYTGVPKAEFKKETFDVTLEPLSFKKEAVLIQAGEYMGQLLEQASLHFFVTARINETRDVLAKQKSTVLTIPEIIIKVRGTQVVGSDMTVIVEFTNPLKETLRNVWVHLDGPGVTRPMKKMFREIRPNSTVQWEEVCRPWVSGHRKLIASMSSDSLRHVYGELDVQIQRRPSM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1717
R free: 0.2305
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 170 mM ammonium sulfate, 85 mM sodium cacodylate, 25.5 % PEG8000, 15 % glycerol
Matthews coefficient: 2.73
Solvent content (%): 54.87
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: 2017-12-20
Crystal structure of c-MET bound by compound 9 (PDB entry 7B43)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 299 residues
Sequence: GNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.2
R free: 0.248
Average B factor: 27.59
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 28 % PEGMME2000, 0.1 M bis-tris pH 6.5
Matthews coefficient: 2.61
Solvent content (%): 52.91
Ligand: 3-[(4-fluorophenyl)methyl]-5-(1-piperidin-4-ylpyrazol-4-yl)-1~{H}-pyrrolo[2,3-b]pyridine (SW5)
Ligand formula: C22 H22 F N5
Ligand molecular weight: 375.442
Ligand SMILES: c1cc(ccc1Cc2c[nH]c3c2cc(cn3)c4cnn(c4)C5CCNCC5)F
Ligand InChI: InChI=1S/C22H22FN5/c23-19-3-1-15(2-4-19)9-17-12-26-22-21(17)10-16(11-25-22)18-13-27-28(14-18)20-5-7-24-8-6-20/h1-4,10-14,20,24H,5-9H2,(H,25,26)
Release date: 2020-12-09
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOOA000666a (PDB entry 5QG4)
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): 1.788
R work: 0.1907
R free: 0.2236
Average B factor: 41.7235
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: 3.31
Solvent content (%): 62.82
Ligand: methyl (1S,3S,4R)-4-hydroxy-3-[(1S)-1-hydroxypropyl]-2-azabicyclo[2.2.2]octane-2-carboxylate (JPD)
Ligand formula: C12 H21 N O4
Ligand molecular weight: 243.299
Ligand SMILES: CCC(C1C2(CCC(N1C(=O)OC)CC2)O)O
Ligand InChI: InChI=1S/C12H21NO4/c1-3-9(14)10-12(16)6-4-8(5-7-12)13(10)11(15)17-2/h8-10,14,16H,3-7H2,1-2H3/t8-,9-,10-,12-/m0/s1
Release date: 2018-10-10
Crystal structure of CREBBP bromodomain complexed with CBP006 (PDB entry 5MQE)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1834
R free: 0.2253
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M potassium thiocyanate, 0.1 M Bis-Tris, pH 5.5, 5% v/v ethylene glycol, 23% PEG3350
Matthews coefficient: 2.02
Solvent content (%): 39.22
Ligand: 4-bromanyl-~{N}-methyl-1~{H}-pyrrole-2-carboxamide (PKU)
Ligand formula: C6 H7 Br N2 O
Ligand molecular weight: 203.037
Ligand SMILES: CNC(=O)c1cc(c[nH]1)Br
Ligand InChI: InChI=1S/C6H7BrN2O/c1-8-6(10)5-2-4(7)3-9-5/h2-3,9H,1H3,(H,8,10)
Release date: 2017-04-19
Crystal structure of human Sirtuin 2 in complex with a selective inhibitor (PDB entry 5Y5N)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 336 residues
Sequence: GSGEADMDFLRNLFSQTLSLGSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDLGETPFDDIATFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.256
R free: 0.252
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 289
Crystal growth procedure: 0.1M Bis-Tris buffer pH 5.5 
15%(w/v) PEG5000 MME
Matthews coefficient: 2.65
Solvent content (%): 53.56
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: 2017-09-06
HIF prolyl hydroxylase 2 (PHD2/EGLN1) K293K/G294E variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/FG2216) (PDB entry 5LBF)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 252 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKIKERTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGEKGVRVELNKPSDSVGKDVF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8995
R work: 0.1595
R free: 0.1847
Average B factor: 51
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 6.5, 1.8 M ammonium sulphate, 2% v/v dioxane, 0.002 M MnCl2
Matthews coefficient: 2.72
Solvent content (%): 54.86
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: 2016-08-31
The crystal structure of CK2alpha in complex with compound 6 (PDB entry 5ORK)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.143
R work: 0.2156
R free: 0.2434
Average B factor: 63.05
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.24
Solvent content (%): 44.98
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2018-02-28
Crystal structure of the 2-iodoporphobilinogen-bound ES2 intermediate form of human hydroxymethylbilane synthase (PDB entry 7CD0)
Macromolecule: Porphobilinogen deaminase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.5.1.61
Sequence length: 361 residues
Sequence: MSGNGNAAATAEENSPKMRVIRVGTRKSQLARIQTDSVVATLKASYPGLQFEIIAMSTTGDKILDTALSKIGEKSLFTKELEHALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPEKSVVGTSSLRRAAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNRVGQILHPEECMYAVGQGALGVEVRAKDQDILDLVGVLHDPETLLRCIAERAFLRHLEGGCSVPVAVHTAMKDGQLYLTGGVWSLDGSDSIQETMQATIHVPAQHEDGPEDDPQLVGITARNIPRGPQLAAQNLGISLANLLLSKGAKNILDVARQLNDAH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.31
R work: 0.2272
R free: 0.2765
Average B factor: 57.52
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, diammonium hydrogen citrate, dithiothreitol
Matthews coefficient: 2.29
Solvent content (%): 46.26
Ligand: 3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid (7J8)
Ligand formula: C40 H46 N4 O16
Ligand molecular weight: 838.81
Ligand SMILES: Cc1c(c(c([nH]1)Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)Cc4c(c(c[nH]4)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
Ligand InChI: InChI=1S/C40H46N4O16/c1-18-23(10-37(53)54)20(3-7-34(47)48)28(42-18)15-31-26(13-40(59)60)22(5-9-36(51)52)30(44-31)16-32-25(12-39(57)58)21(4-8-35(49)50)29(43-32)14-27-24(11-38(55)56)19(17-41-27)2-6-33(45)46/h17,41-44H,2-16H2,1H3,(H,45,46)(H,47,48)(H,49,50)(H,51,52)(H,53,54)(H,55,56)(H,57,58)(H,59,60)
Release date: 2021-03-17
FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl [(4R,5E,8S)-11-chloro-8-[(2,6-difluoro-4-methylbenzene-1-carbonyl)amino]-4-methyl-2-oxo-1,3,4,7,8,10-hexahydro-2H-12,9-(azeno)-1,10-benzodiazacyclotetradecin-15-yl]carbamate (PDB entry 5Q0H)
Macromolecule: Coagulation factor XI
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.168
R free: 0.21
Average B factor: 30.41
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM sodium acetate, pH 4.6, 25% (w/v) MePEG2000, 200 mM ammonium sulfate, then transferred to 100 mM Tris-HCl, pH 7.0, 25% (w/v) MePEG2000, 200 MM ammonium sulfate
Matthews coefficient: 3.43
Solvent content (%): 64.16
Ligand: methyl [(4R,5E,8S)-11-chloro-8-[(2,6-difluoro-4-methylbenzene-1-carbonyl)amino]-4-methyl-2-oxo-1,3,4,7,8,10-hexahydro-2H-12,9-(azeno)-1,10-benzodiazacyclotetradecin-15-yl]carbamate (9F1)
Ligand formula: C27 H26 Cl F2 N5 O4
Ligand molecular weight: 557.976
Ligand SMILES: Cc1cc(c(c(c1)F)C(=O)NC2CC=CC(CC(=O)Nc3cc(ccc3-c4c([nH]c2n4)Cl)NC(=O)OC)C)F
Ligand InChI: InChI=1S/C27H26ClF2N5O4/c1-13-5-4-6-19(33-26(37)22-17(29)9-14(2)10-18(22)30)25-34-23(24(28)35-25)16-8-7-15(31-27(38)39-3)12-20(16)32-21(36)11-13/h4-5,7-10,12-13,19H,6,11H2,1-3H3,(H,31,38)(H,32,36)(H,33,37)(H,34,35)/b5-4+/t13-,19-/m0/s1
Release date: 2017-07-12
Human JAK2 JH1 domain in complex with Baricitinib (PDB entry 6WTO)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 309 residues
Sequence: MAFEDRDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAGGSGSENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.1973
R free: 0.218
Average B factor: 45.2045
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 1.6-2.4 M sodium malonate, pH 5
Matthews coefficient: 2.1
Solvent content (%): 41.39
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: 2021-05-05
Human Aprataxin (Aptx) R199H bound to RNA-DNA, AMP and Zn product complex (PDB entry 6CVP)
Macromolecule: Aprataxin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.11.7
Sequence length: 182 residues
Sequence: GSHMGHWSQGLKISMQDPKMQVYKDEQVVVIKDKYPKAHYHWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIVDFAGSSKLRFRLGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFNTEYFLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCHECQQLLPSIPQLKEHLRKHWTQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.999
R work: 0.1644
R free: 0.2138
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES, 20% w/v polyethylene glycol 3350
Matthews coefficient: 2.68
Solvent content (%): 54.05
Ligand: ADENOSINE MONOPHOSPHATE (AMP)
Ligand formula: C10 H14 N5 O7 P
Ligand molecular weight: 347.221
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2018-07-04
Crystal structure of human SET and MYND Domain Containing protein 2 with MTF1497 (PDB entry 6CBX)
Macromolecule: N-lysine methyltransferase SMYD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 434 residues
Sequence: GMRAEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLEFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIESH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.1797
R free: 0.2229
Average B factor: 31.655
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG 3350, 0.2 M NH4SO4
Matthews coefficient: 2.19
Solvent content (%): 43.85
Ligand: UNKNOWN ATOM OR ION (UNX)
Ligand formula: X
Ligand SMILES: *
Release date: 2018-03-14
Crystal structure of SND1 in complex with C-26-A6 (PDB entry 7KNX)
Macromolecule: Staphylococcal nuclease domain-containing protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.31.1
Sequence length: 324 residues
Sequence: MGSSHHHHHHSSGENLYFQGVPTVQRGIIKMVLSGCAIIVRGQPRGGPPPERQINLSNIRAGNLARRAAKDTPDEPWAFPAREFLRKKLIGKEVCFTIENKTPQGREYGMIYLGKDTNGENIAESLVAEGLATRREGMRANNPEQNRLSECEEQAKAAKKGMWSEGNGSHTIRDLKYTIENPRHFVDSHHQKPVNAIIEHVRDGSVVRALLLPDYYLVTVMLSGIKCPTFRRETPEPFAAEAKFFTESRLLQRDVQIILESCHNQNILGTILHPNGNITELLLKEGFARCVDWSIAVYTRGAEKLRAAERFAKERRLRIWRDYV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2596
R free: 0.329
Average B factor: 55.537
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 MES-NaOH pH 6.2, 0.9 M trisodium citrate
Matthews coefficient: 2.49
Solvent content (%): 50.53
Ligand: TYROSINE (TYR)
Ligand formula: C9 H11 N O3
Ligand molecular weight: 181.189
Ligand SMILES: c1cc(ccc1CC(C(=O)O)N)O
Ligand InChI: InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/t8-/m0/s1
Release date: 2021-12-08
Cyclophilin A complexed with tri-vector ligand 7. (PDB entry 6GJP)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.17495
R free: 0.23726
Average B factor: 29.249
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 279.15
Crystal growth procedure: PEG 8000, Tris-HCl
Matthews coefficient: 2.82
Solvent content (%): 56.38
Ligand: ethyl 2-[[(4-aminophenyl)methyl-(cyclopropylmethyl)carbamoyl]amino]ethanoate (F0T)
Ligand formula: C16 H23 N3 O3
Ligand molecular weight: 305.372
Ligand SMILES: CCOC(=O)CNC(=O)N(Cc1ccc(cc1)N)CC2CC2
Ligand InChI: InChI=1S/C16H23N3O3/c1-2-22-15(20)9-18-16(21)19(10-12-3-4-12)11-13-5-7-14(17)8-6-13/h5-8,12H,2-4,9-11,17H2,1H3,(H,18,21)
Release date: 2018-11-07
HUMAN DNA POLYMERASE ETA EXTENSION COMPLEX WITH AN INCOMING DCTP (PDB entry 8EVF)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.87
R work: 0.2042
R free: 0.2512
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES PH 5.5, 5mM calcium chloride, 15-22% PEG 2000 MME
Matthews coefficient: 2.13
Solvent content (%): 42.34
Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
Release date: 2023-08-02
Structure of ZNRF3 ECD bound to peptide MK1-3.6.10 (PDB entry 8G4Y)
Macromolecule: E3 ubiquitin-protein ligase ZNRF3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 178 residues
Sequence: GSTKETAFVEVVLFESSPSGDYTTYTTGLTGRFSRAGATLSAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHRPPRQPTEYFDMGNSDYKDDDDK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.2134
R free: 0.2361
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M sodium citrate pH 4.5, 20% PEG 4000 plus silver bullet A5 (Hampton Research)
Matthews coefficient: 2.28
Solvent content (%): 46.07
Release date: 2023-12-20