satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human MMP-7 in complex with inhibitor (PDB entry 8K4Z)
Macromolecule: Matrilysin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.23
Sequence length: 175 residues
Sequence: MGYSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHQLGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYGKRSNSRKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.203
R free: 0.2392
Average B factor: 18.838
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% w/v Polyethylene glycol 3350,  100mM Bis-Tris propane pH7.5,  200mM Sodium iodide
Matthews coefficient: 2.16
Solvent content (%): 42.93
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: 2024-04-17
Human FKBP12 in complex with (1S,5S,6R)-10-((S)-3,5-dichloro-N-methylphenylsulfonimidoyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-2-one (PDB entry 8CHI)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 107 residues
Sequence: GVQVETISPGDGRTFPKRGQTVVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.178
R free: 0.2144
Average B factor: 21.329
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.4M Na/K tartrate, 0.2 M ammonium citrate, 0.1M MES pH 6.5
Matthews coefficient: 3.3
Solvent content (%): 62.72
Ligand: (1S,5S,6R)-10-[S-[3,5-bis(chloranyl)phenyl]-N-methyl-sulfonimidoyl]-5-ethenyl-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one (UMR)
Ligand formula: C23 H26 Cl2 N4 O2 S
Ligand molecular weight: 493.449
Ligand SMILES: CN=S(=O)(c1cc(cc(c1)Cl)Cl)N2C3CCCC2C(=O)N(CC3C=C)Cc4ccccn4
Ligand InChI: InChI=1S/C23H26Cl2N4O2S/c1-3-16-14-28(15-19-7-4-5-10-27-19)23(30)22-9-6-8-21(16)29(22)32(31,26-2)20-12-17(24)11-18(25)13-20/h3-5,7,10-13,16,21-22H,1,6,8-9,14-15H2,2H3/t16-,21+,22-,32-/m0/s1
Release date: 2023-09-06
Crystal structure of the human METTL3-METTL14 complex bound to SAM (PDB entry 5L6E)
Macromolecule: N6-adenosine-methyltransferase 70 kDa subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.62
Sequence length: 227 residues
Sequence: ALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.901
R work: 0.1572
R free: 0.183
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 22 % PEG 3350, 300 mM Mg acetate
Matthews coefficient: 2.24
Solvent content (%): 45.19
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2016-10-12
X-ray structure of human PPARalpha ligand binding domain-bezafibrate-SRC1 coactivator peptide co-crystals obtained by soaking (PDB entry 7BPZ)
Macromolecule: Peroxisome proliferator-activated receptor alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 273 residues
Sequence: GSHMTADLKSLAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYRDMY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.43
R work: 0.2009
R free: 0.2421
Average B factor: 62.7159
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris (pH 8.5), 25 %(w/v) PEG3350
Matthews coefficient: 2.8
Solvent content (%): 56.1
Ligand: 2-[P-[2-P-CHLOROBENZAMIDO)ETHYL]PHENOXY]-2-METHYLPROPIONIC ACID (PEM)
Ligand formula: C19 H20 Cl N O4
Ligand molecular weight: 361.819
Ligand SMILES: CC(C)(C(=O)O)Oc1ccc(cc1)CCNC(=O)c2ccc(cc2)Cl
Ligand InChI: InChI=1S/C19H20ClNO4/c1-19(2,18(23)24)25-16-9-3-13(4-10-16)11-12-21-17(22)14-5-7-15(20)8-6-14/h3-10H,11-12H2,1-2H3,(H,21,22)(H,23,24)
Release date: 2020-11-11
Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening (PDB entry 8JUC)
Macromolecule: Ubiquitin-conjugating enzyme E2 T
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 156 residues
Sequence: GSMQRASRLKRELHMLATEPPPGITCWQDKDQMDDLRAQILGGANTPYEKGVFKLEVIIPERYPFEPPQIRFLTPIYHPNIDSAGRICLDVLKLPPKGAWRPSLNIATVLTSIQLLMSEPNPDDPLMADISSEFKYNKPAFLKNARQWTEKHARQK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.54
R work: 0.2179
R free: 0.2367
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 3.5 M Sodium formate pH 7.0
Matthews coefficient: 3.84
Solvent content (%): 67.95
Ligand: 7-methyl-2-(trifluoromethyl)-3~{H}-[1,2,4]triazolo[1,5-a]pyridin-5-one (V23)
Ligand formula: C8 H6 F3 N3 O
Ligand molecular weight: 217.148
Ligand SMILES: CC1=CC(=O)N2C(=C1)N=C(N2)C(F)(F)F
Ligand InChI: InChI=1S/C8H6F3N3O/c1-4-2-5-12-7(8(9,10)11)13-14(5)6(15)3-4/h2-3H,1H3,(H,12,13)
Release date: 2024-02-28
Human DNMT3B PWWP domain in complex with N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine (PDB entry 5NV7)
Macromolecule: DNA (cytosine-5)-methyltransferase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.37
Sequence length: 150 residues
Sequence: EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.568
R work: 0.1979
R free: 0.2329
Average B factor: 56.54
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Matthews coefficient: 3.8
Solvent content (%): 67.62
Ligand: N1-(2-hydroxyethyl)-2-methyl-1,2-propanediamine (9AK)
Ligand formula: C6 H16 N2 O
Ligand molecular weight: 132.204
Ligand SMILES: CC(C)(CNCCO)N
Ligand InChI: InChI=1S/C6H16N2O/c1-6(2,7)5-8-3-4-9/h8-9H,3-5,7H2,1-2H3
Release date: 2018-05-30
Crystal structure of FGFR4(V550M) kinase domain with 10z (PDB entry 7YBX)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: LLAGLVSLDLPLDPLWEFPRDRLVLGKPLGEGAFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIMECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDEVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.233
R work: 0.1796
R free: 0.2203
Average B factor: 27.0086
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris (pH 4.5), 0.2 M Li2SO4, 16-19 % PEG 3350
Matthews coefficient: 2.24
Solvent content (%): 45.03
Ligand: ~{N}-[4-[(1~{R})-1-[3,5-bis(chloranyl)pyridin-4-yl]ethoxy]-5-cyano-pyridin-2-yl]-6-bromanyl-5-(hydroxymethyl)-1-(2-morpholin-4-ylethyl)pyrrolo[3,2-b]pyridine-3-carboxamide (IH7)
Ligand formula: C28 H24 Br Cl2 N7 O4
Ligand molecular weight: 673.345
Ligand SMILES: CC(c1c(cncc1Cl)Cl)Oc2cc(ncc2C#N)NC(=O)c3cn(c4c3nc(c(c4)Br)C=O)CCN5CCOCC5
Ligand InChI: InChI=1S/C28H24BrCl2N7O4/c1-16(26-20(30)12-33-13-21(26)31)42-24-9-25(34-11-17(24)10-32)36-28(40)18-14-38(3-2-37-4-6-41-7-5-37)23-8-19(29)22(15-39)35-27(18)23/h8-9,11-16H,2-7H2,1H3,(H,34,36,40)/t16-/m1/s1
Release date: 2022-11-16
Human angiogenin PD variant K54R (PDB entry 5M9G)
Macromolecule: Angiogenin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27
Sequence length: 124 residues
Sequence: MQDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIRAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFRRP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.22015
R free: 0.27057
Average B factor: 48.37
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 289
Crystal growth procedure: 0.2 M Na/K tartrate
0.1 M HEPES
3% propanol
20% PEG 8000
Matthews coefficient: 3.18
Solvent content (%): 61.35
Ligand: D(-)-TARTARIC ACID (TAR)
Ligand formula: C4 H6 O6
Ligand molecular weight: 150.087
Ligand SMILES: C(C(C(=O)O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/t1-,2-/m0/s1
Release date: 2017-02-22
Crystal structure of MELK in complex with an inhibitor (PDB entry 5MAH)
Macromolecule: Maternal embryonic leucine zipper kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 347 residues
Sequence: GPKDYDELLKYYELHETIGTGGFAKVKLACHILTGEMVAIKIMDKNTLGSDLPRIKTEIEALKNLRHQHICQLYHVLETANKIFMVLEYCPGGELFDYIISQDRLSEEETRVVFRQIVSAVAYVHSQGYAHRDLKPENLLFDEYHKLKLIDFGLCAKPKGNKDYHLQTCCGSLAYAAPELIQGKSYLGSEADVWSMGILLYVLMCGFLPFDDDNVMALYKKIMRGKYDVPKWLSPSSILLLQQMLQVDPKKRISMKNLLNHPWIMQDYNYPVEWQSKNPFIHLDDDCVTELSVHHRNNRQTMEDLISLWQYDHLTATYLLLLAKKARGKPVRLRLSSFSCGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.18284
R free: 0.23715
Average B factor: 38.418
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 10-20% PEG 3350 or PEG 4000, 0.1 M BIS TRIS pH 6.5, 0.6M NaCl
Matthews coefficient: 2.15
Solvent content (%): 42.76
Ligand: ~{N}-methyl-4-[[4-[[3-[methyl(methylsulfonyl)amino]pyrazin-2-yl]methylamino]-5-(trifluoromethyl)pyrimidin-2-yl]amino]benzamide (7KD)
Ligand formula: C20 H21 F3 N8 O3 S
Ligand molecular weight: 510.493
Ligand SMILES: CNC(=O)c1ccc(cc1)Nc2ncc(c(n2)NCc3c(nccn3)N(C)S(=O)(=O)C)C(F)(F)F
Ligand InChI: InChI=1S/C20H21F3N8O3S/c1-24-18(32)12-4-6-13(7-5-12)29-19-28-10-14(20(21,22)23)16(30-19)27-11-15-17(26-9-8-25-15)31(2)35(3,33)34/h4-10H,11H2,1-3H3,(H,24,32)(H2,27,28,29,30)
Release date: 2017-12-06
Crystal structure of EGFR 696-1022 T790M in complex with AZD9291 prepared by co-crystallization (PDB entry 6JX0)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GAMGGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.1915
R free: 0.2217
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M Ammonium tartrate dibasic, 0.1 M BIS-TRIS propane pH 7.0
Matthews coefficient: 4.25
Solvent content (%): 71.09
Ligand: N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxy-5-{[4-(1-methyl-1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)prop-2-enamide (YY3)
Ligand formula: C28 H33 N7 O2
Ligand molecular weight: 499.607
Ligand SMILES: Cn1cc(c2c1cccc2)c3ccnc(n3)Nc4cc(c(cc4OC)N(C)CCN(C)C)NC(=O)C=C
Ligand InChI: InChI=1S/C28H33N7O2/c1-7-27(36)30-22-16-23(26(37-6)17-25(22)34(4)15-14-33(2)3)32-28-29-13-12-21(31-28)20-18-35(5)24-11-9-8-10-19(20)24/h7-13,16-18H,1,14-15H2,2-6H3,(H,30,36)(H,29,31,32)
Release date: 2020-04-22
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000438a (PDB entry 7GSB)
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): 1.72
R work: 0.1885
R free: 0.2249
Average B factor: 37.725
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: 3.34
Solvent content (%): 63.15
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
HIF prolyl hydroxylase 2 (PHD2/EGLN1) P317R variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9) (PDB entry 5LAT)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 252 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNRNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGEKGVRVELNKPSDSVGKDVF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1504
R free: 0.1659
Average B factor: 33
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M tri-sodium citrate pH 5.6, 20% PEG 4000, 20% 2-propanol
Matthews coefficient: 2.87
Solvent content (%): 57.19
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
PDE10 complexed with 6-chloro-2-cyclopropyl-5-methyl-pyrimidin-4-amine (PDB entry 5C28)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 362 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1704
R free: 0.1956
Average B factor: 22.35
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 100mM HEPES, 20% PEG3350, 200mM MgCl2, and 10mM 2-Mercaptoethanol
Matthews coefficient: 1.88
Solvent content (%): 34.42
Ligand: 6-chloro-2-cyclopropyl-5-methylpyrimidin-4-amine (4XV)
Ligand formula: C8 H10 Cl N3
Ligand molecular weight: 183.638
Ligand SMILES: Cc1c(nc(nc1Cl)C2CC2)N
Ligand InChI: InChI=1S/C8H10ClN3/c1-4-6(9)11-8(5-2-3-5)12-7(4)10/h5H,2-3H2,1H3,(H2,10,11,12)
Release date: 2015-09-30
The tandem SH2 domains of SYK (PDB entry 7Q63)
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: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.217
R free: 0.2643
Average B factor: 52.278
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 200 mM, potassium thiocyanate, 12.5% glycerol, 23% PEG3350
Matthews coefficient: 2.68
Solvent content (%): 54.12
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: 2021-11-24
Human SIRT2 crystal structure in complex with BHJH-TM1 (PDB entry 4R8M)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 319 residues
Sequence: MDFLRNLFSQTLSLGSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.22091
R free: 0.27332
Average B factor: 46.717
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 25%(v/v) PEG3350, 0.1M Hepes buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 2.08
Solvent content (%): 40.96
Ligand: tridecanethial (3LX)
Ligand formula: C13 H26 S
Ligand molecular weight: 214.411
Ligand SMILES: CCCCCCCCCCCCC=S
Ligand InChI: InChI=1S/C13H26S/c1-2-3-4-5-6-7-8-9-10-11-12-13-14/h13H,2-12H2,1H3
Release date: 2015-03-11
Crystal structure of FGFR4 kinase domain with 10d (PDB entry 7YC1)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 311 residues
Sequence: GPLLAGLVSLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDEVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.535
R work: 0.1829
R free: 0.2259
Average B factor: 31.4045
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris (pH 4.5), 0.2 M Li2SO4, 16-19 % PEG 3350
Matthews coefficient: 2.22
Solvent content (%): 44.59
Ligand: ~{N}-[5-cyano-4-(2-methoxyethylamino)pyridin-2-yl]-5-methanoyl-1-propyl-pyrrolo[3,2-b]pyridine-3-carboxamide (IIQ)
Ligand formula: C21 H22 N6 O3
Ligand molecular weight: 406.438
Ligand SMILES: CCCn1cc(c2c1ccc(n2)C=O)C(=O)Nc3cc(c(cn3)C#N)NCCOC
Ligand InChI: InChI=1S/C21H22N6O3/c1-3-7-27-12-16(20-18(27)5-4-15(13-28)25-20)21(29)26-19-9-17(23-6-8-30-2)14(10-22)11-24-19/h4-5,9,11-13H,3,6-8H2,1-2H3,(H2,23,24,26,29)
Release date: 2022-11-16
Ligand binding to HDAC2 (PDB entry 7ZZW)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 498 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEEFSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGTKSEQLSNPGSSGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.1643
R free: 0.1891
Average B factor: 31.794
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 41% PEG 300
0.1M pH=8.8 CHES/NaOH
Matthews coefficient: 1.86
Solvent content (%): 33.7
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: 2022-09-21
Crystal structure of human heme oxygenase 1 H25R with biliverdin bound (PDB entry 5BTQ)
Macromolecule: Heme oxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.3
Sequence length: 237 residues
Sequence: GSHMMERPQPDSMPQDLSEALKEATKEVRTQAENAEFMRNFQKGQVTRDGFKLVMASLYHIYVALEEEIERNKESPVFAPVYFPEELHRKAALEQDLAFWYGPRWQEVIPYTPAMQRYVKRLHEVGRTEPELLVAHAYTRYLGDLSGGQVLKKIAQKALDLPSSGEGLAFFTFPNIASATKFKQLYRSRMNSLEMTPAVRQRVIEEAKTAFLLNIQLFEELQELLTHDTKDQSPSRA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.18269
R free: 0.22818
Average B factor: 30.208
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 100mM HEPES
2.1M Ammonium sulfate
0.9% 1,6-hexanediol
Matthews coefficient: 2.21
Solvent content (%): 44.35
Ligand: BILIVERDINE IX ALPHA (BLA)
Ligand formula: C33 H34 N4 O6
Ligand molecular weight: 582.646
Ligand SMILES: Cc1c(c([nH]c1C=C2C(=C(C(=O)N2)C=C)C)C=C3C(=C(C(=N3)C=C4C(=C(C(=O)N4)C)C=C)C)CCC(=O)O)CCC(=O)O
Ligand InChI: InChI=1S/C33H34N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h7-8,13-15,34H,1-2,9-12H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14-,29-15-
Release date: 2016-06-08
Structure of MAPK14 with bound the KIM domain of the Toxoplasma protein GRA24 (PDB entry 5ETA)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2188
R free: 0.2903
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M MgCl2, 0.1M Tris/HCl pH 8.5, 25-28% PEG 3350
Matthews coefficient: 2.39
Solvent content (%): 48.61
Release date: 2016-10-26