satarupa22/MacromolecularLigandDB huggingface dataset:
HIGH-SALT STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR 4P (PDB entry 5OMY)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 391 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPTPSPLGPLAGSPVIAAANPLGMPVPAAAGAQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1925
R free: 0.2208
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 90 MIKROLITER ENZYME STOCK SOLUTION (6
MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10
MIKROLITER 4P STOCK SOLUTION (10 MM 4P IN DMSO). THIS
MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE
RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 4.2 M
NACL, 0.1 M CITRIC ACID, PH 5.5. PRIOR TO EQUILIBRATION THE
CRYSTALLIZATION DROP WAS COMPOSED OF 1 MIKROLITER RESERVOIR
SOLUTION PLUS 1 MIKROLITER ENZYME/4P MIXTURE., VAPOR DIFFUSION,
SITTING DROP, TEMPERATURE 293.15K
Matthews coefficient: 1.94
Solvent content (%): 36.66
Ligand: 4-(3-methylbut-2-enoxy)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione (9YE)
Ligand formula: C23 H25 N O3
Ligand molecular weight: 363.45
Ligand SMILES: CC(C)n1c2c(c3c1-c4c(cccc4OCC=C(C)C)C3=O)C(=O)CCC2
Ligand InChI: InChI=1S/C23H25NO3/c1-13(2)11-12-27-18-10-5-7-15-19(18)22-21(23(15)26)20-16(24(22)14(3)4)8-6-9-17(20)25/h5,7,10-11,14H,6,8-9,12H2,1-4H3
Release date: 2017-12-27
Crystal structure of Tdp1 catalytic domain in complex with compound XZ502 (PDB entry 6DJF)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.188
R free: 0.2124
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M MOPS/HEPES-Na pH 7.5
10% w/v PEG 8000
20% v/v ethylene glycol
0.03M sodium fluoride
0.03M sodium bromide
0.03M sodium iodide
Matthews coefficient: 2.46
Solvent content (%): 49.95
Ligand: 4-hydroxyquinoline-3,8-dicarboxylic acid (GNV)
Ligand formula: C11 H7 N O5
Ligand molecular weight: 233.177
Ligand SMILES: c1cc2c(c(c1)C(=O)O)ncc(c2O)C(=O)O
Ligand InChI: InChI=1S/C11H7NO5/c13-9-5-2-1-3-6(10(14)15)8(5)12-4-7(9)11(16)17/h1-4H,(H,12,13)(H,14,15)(H,16,17)
Release date: 2019-05-29
JAK2 JH1 in complex with BL2-096 (PDB entry 6VNC)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 308 residues
Sequence: HHHHHHHHENLYFQGDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.226
R free: 0.2686
Average B factor: 71.7999
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% PEG 3350
Matthews coefficient: 3.06
Solvent content (%): 59.79
Ligand: (3R)-3-cyclopentyl-3-[4-(2-{[4-(piperidin-4-yl)phenyl]amino}-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile (R6V)
Ligand formula: C28 H32 N8
Ligand molecular weight: 480.607
Ligand SMILES: c1cc(ccc1C2CCNCC2)Nc3nc(c4cc[nH]c4n3)c5cnn(c5)C(CC#N)C6CCCC6
Ligand InChI: InChI=1S/C28H32N8/c29-13-9-25(21-3-1-2-4-21)36-18-22(17-32-36)26-24-12-16-31-27(24)35-28(34-26)33-23-7-5-19(6-8-23)20-10-14-30-15-11-20/h5-8,12,16-18,20-21,25,30H,1-4,9-11,14-15H2,(H2,31,33,34,35)/t25-/m1/s1
Release date: 2021-02-17
Crystal structure of human GRP78 in complex with 8-bromoadenosine (PDB entry 6DFO)
Macromolecule: Endoplasmic reticulum chaperone BiP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.10
Sequence length: 382 residues
Sequence: DVGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREGEKNILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFYEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.54
R work: 0.187
R free: 0.251
Average B factor: 41.31
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: Triclinic crystals of apo GRP78 were observed in 0.1 M Tris-HCl, 25% PEG3350, 0.1 M sodium/potassium tartrate. Initial crystals were then microseeded in 25% PEG3350, 0.1 M Tris-HCl, 0.2 M sodium chloride. These new apo monoclinic crystals were soaked with 5 mM 8-bromoadenosine for one week.
Matthews coefficient: 2.18
Solvent content (%): 43.63
Ligand: 8-bromoadenosine (GBA)
Ligand formula: C10 H12 Br N5 O4
Ligand molecular weight: 346.137
Ligand SMILES: c1nc(c2c(n1)n(c(n2)Br)C3C(C(C(O3)CO)O)O)N
Ligand InChI: InChI=1S/C10H12BrN5O4/c11-10-15-4-7(12)13-2-14-8(4)16(10)9-6(19)5(18)3(1-17)20-9/h2-3,5-6,9,17-19H,1H2,(H2,12,13,14)/t3-,5-,6-,9-/m1/s1
Release date: 2019-05-15
PDE10 complexed with 5-chloro-N-[(2,4-dimethylthiazol-5-yl)methyl]pyrazolo[1,5-a]pyrimidin-7-amine (PDB entry 5DH4)
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: 345 residues
Sequence: GSHMSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2032
R free: 0.2325
Average B factor: 57.67
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 100mM HEPES pH 7.0, 20% PEG3350, 200mM MgCl2, and 10mM 2-Mercaptoethanol
Matthews coefficient: 1.98
Solvent content (%): 37.9
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: 2016-01-27
Crystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in CCACCA (PDB entry 4X4T)
Macromolecule: CCA-adding enzyme
Type: Protein, polypeptide(L)
Source organism: Archaeoglobus fulgidus DSM 4304
EC number: 2.7.7.72
Sequence length: 457 residues
Sequence: MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKDSNSSSVDKLAAALEHHHHHH
Oligomeric state: Homo 4-mer
Stoichiometry: A4
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.186
R free: 0.229
Average B factor: 70.4
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 20% PEG3350, 0.2M NaK tartrate
Matthews coefficient: 2.57
Solvent content (%): 52.1
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2015-02-11
FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl [(3R,7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-3-ethyl-2-oxo-1,2,3,4,5,6,7,9-octahydro-11,8-(azeno)-1,9-benzodiazacyclotridecin-14-yl]carbamate (PDB entry 5Q0G)
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): 2.6
R work: 0.1837
R free: 0.2293
Average B factor: 20.7
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: 3.45
Solvent content (%): 64.32
Ligand: methyl [(3R,7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-3-ethyl-2-oxo-1,2,3,4,5,6,7,9-octahydro-11,8-(azeno)-1,9-benzodiazacyclotridecin-14-yl]carbamate (9F7)
Ligand formula: C29 H30 Cl N9 O4
Ligand molecular weight: 604.059
Ligand SMILES: CCC1CCCC(c2[nH]cc(n2)-c3ccc(cc3NC1=O)NC(=O)OC)NC(=O)C=Cc4cc(ccc4n5cnnn5)Cl
Ligand InChI: InChI=1S/C29H30ClN9O4/c1-3-17-5-4-6-22(34-26(40)12-7-18-13-19(30)8-11-25(18)39-16-32-37-38-39)27-31-15-24(35-27)21-10-9-20(33-29(42)43-2)14-23(21)36-28(17)41/h7-17,22H,3-6H2,1-2H3,(H,31,35)(H,33,42)(H,34,40)(H,36,41)/b12-7+/t17-,22+/m1/s1
Release date: 2017-07-12
Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN14770 (PDB entry 6NJJ)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 370 residues
Sequence: MSIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQAPAPPLDEQNRDSQGNQVSEFISNTFLDENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.167
R free: 0.214
Average B factor: 31.06
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.3
Crystallization temperature (K): 298
Crystal growth procedure: 8.8MG/ML VCID7620 + 0.5MM BPN-
 014770 (EBSI4045) IN A PROTEIN SOLUTION CONTAINING 10MM HEPES
 PH 7.5, 100MM NACL, 1MM DTT, 0.1MM ZNCL2, 0.1MM MGCL2 (BATCH
 1214057) AGAINST OPTIMIZATION SCREEN TET_MPC8_JCH7 (OPT SCREEN
 BASED ON MORPHEUS C8 AND JCSG H7); 6.25% W/V PEG1,000, 20.91%
 W/V PEG3350, 6.25% W/V MPD, 0.2M AMMONIUM SULFATE, 0.1MM BIS-
 TRIS PH 6.3, CRYO-PROTECTED - 20% ETHYLENE GLYCOL, CRYSTAL
 TRACKING ID 247599D11 (WEV9-9), PH 6.30, VAPOR DIFFUSION,
 SITTING DROP, TEMPERATURE 289K
Matthews coefficient: 2.14
Solvent content (%): 42.65
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: 2019-05-08
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5-(PCP)2-IP4 (PDB entry 5BYA)
Macromolecule: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.4.21
Sequence length: 330 residues
Sequence: GSFTERQIVVGICSMAKKSKSKPMKEILERISLFKYITVVVFEEEVILNEPVENWPLCDCLISFHSKGFPLDKAVAYAKLRNPFVINDLNMQYLIQDRREVYSILQAEGILLPRYAILNRDPNNPKECNLIEGEDHVEVNGEVFQKPFVEKPVSAEDHNVYIYYPTSAGGGSQRLFRKIGSRSSVYSPESNVRKTGSYIYEEFMPTDGTDVKVYTVGPDYAHAEARKSPALDGKVERDSEGKEVRYPVILNAREKLIAWKVCLAFKQTVCGFDLLRANGQSYVCDVNGFSFVKNSMKYYDDCAKILGNIVMRELAPQFHIPWSIPLEAED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1413
R free: 0.199
Average B factor: 22.557
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM ATP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M sodium acetate, pH 5.2 at 4 oC overnight, while ATP in the crystals was hydrolyzed to ADP. The crystals were soaked under the above stabilizing buffer for three days with 2 mM analog.
Matthews coefficient: 2.79
Solvent content (%): 55.96
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: 2015-07-22
Nek2 kinase bound to inhibitor 96 (PDB entry 6SGI)
Macromolecule: Serine/threonine-protein kinase Nek2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 279 residues
Sequence: MPSRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2129
R free: 0.2658
Average B factor: 42.66
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Tris pH 8.5, 3% PEG 8000
Matthews coefficient: 2.73
Solvent content (%): 54.91
Ligand: 4-[(6-ethyl-7~{H}-purin-2-yl)amino]benzenesulfonamide (LCB)
Ligand formula: C13 H14 N6 O2 S
Ligand molecular weight: 318.354
Ligand SMILES: CCc1c2c(nc[nH]2)nc(n1)Nc3ccc(cc3)S(=O)(=O)N
Ligand InChI: InChI=1S/C13H14N6O2S/c1-2-10-11-12(16-7-15-11)19-13(18-10)17-8-3-5-9(6-4-8)22(14,20)21/h3-7H,2H2,1H3,(H2,14,20,21)(H2,15,16,17,18,19)
Release date: 2020-06-17
Human dihydroorotase mutant F1563T co-crystallized with carbamoyl aspartate at pH 7.0 (PDB entry 6HFP)
Macromolecule: CAD protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.5.5
Sequence length: 393 residues
Sequence: GPMTSQKLVRLPGLIDVHVHLREPGGTHKEDFASGTAAALAGGITMVCAMPNTRPPIIDGPALALAQKLAEAGARCDFALFLGASSENAGTLGTVAGSAAGLKLYLNETTSELRLDSVVQWMEHFETWPSHLPIVAHAEQQTVAAVLMVAQLTQRSVHICHVARKEEILLIKAAKARGLPVTCEVAPHHLFLSHDDLERLGPGKGEVRPELGSRQDVEALWENMAVIDCFASDHAPHTLEEKCGSRPPPGFPGLETMLPLLLTAVSEGRLSLDDLLQRLHHNPRRIFHLPPQEDTYVEVDLEHEWTIPSHMPFSKAHWTPFEGQKVKGTVRRVVLRGEVAYIDGQVLVPPGYGQDVRKWPQGAVPQLPPSAPATSEMTTTPERPRRGIPGLPD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.19822864429
R work: 0.121748467499
R free: 0.1366740553
Average B factor: 21.0978390917
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Protein at 2-3 mg/ml in 20 mM Tris pH 8, 0.15 M NaCl, 0.02 mM zinc sulfate, 0.2 mM TCEP with 4 mM carbamoyl asparate.
Mother liquor: 2.5-3 M potassium formate, 0.1 M HEPES pH 7.0
Matthews coefficient: 2.53
Solvent content (%): 51.3
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: 2018-10-24
STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ARYL KETONE INHIBITOR (PDB entry 6XDM)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 376 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1674
R free: 0.1886
Average B factor: 22.76
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
Matthews coefficient: 2.48
Solvent content (%): 50.49
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: 2020-07-29
Human APE1 phosphorothioate substrate complex with Mn2+ (PDB entry 5DG0)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 276 residues
Sequence: ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.166
R free: 0.205
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 10% Peg 20000, 100 mM sodium citrate, 200 mM MgCl2
Matthews coefficient: 2.56
Solvent content (%): 52.03
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: 2015-10-14
Factor XIA in complex with the inhibitor methyl (4-{6-[(1S)-2-[(3R)-1-acetylpiperidin-3-yl]-1-({(2E)-3-[5-chloro-2- (1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)ethyl]-3-chloropyridazin-4-yl}phenyl) carbamate (PDB entry 6C0S)
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): 2.35
R work: 0.195
R free: 0.226
Average B factor: 37
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: 3.59
Solvent content (%): 65.75
Ligand: methyl (4-{6-[(1S)-2-[(3R)-1-acetylpiperidin-3-yl]-1-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)ethyl]-3-chloropyridazin-4-yl}phenyl)carbamate (EEJ)
Ligand formula: C31 H31 Cl2 N9 O4
Ligand molecular weight: 664.542
Ligand SMILES: CC(=O)N1CCCC(C1)CC(c2cc(c(nn2)Cl)c3ccc(cc3)NC(=O)OC)NC(=O)C=Cc4cc(ccc4n5cnnn5)Cl
Ligand InChI: InChI=1S/C31H31Cl2N9O4/c1-19(43)41-13-3-4-20(17-41)14-26(36-29(44)12-7-22-15-23(32)8-11-28(22)42-18-34-39-40-42)27-16-25(30(33)38-37-27)21-5-9-24(10-6-21)35-31(45)46-2/h5-12,15-16,18,20,26H,3-4,13-14,17H2,1-2H3,(H,35,45)(H,36,44)/b12-7+/t20-,26+/m1/s1
Release date: 2018-03-07
Crystal structure of PTPN3 (PTPH1) H812F, M883G mutant in complex with Eps15 pTyr849 peptide (PDB entry 4RH9)
Macromolecule: Epidermal growth factor receptor substrate 15
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 9 residues
Sequence: FSAYPSEED
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.598
R work: 0.1945
R free: 0.2264
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris-HCl, 21% PEG 8000, 5% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Matthews coefficient: 1.91
Solvent content (%): 35.46
Release date: 2015-03-11
MITOGEN ACTIVATED PROTEIN KINASE 7 IN COMPLEX WITH INHIBITOR (PDB entry 4ZSL)
Macromolecule: Mitogen-activated protein kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 341 residues
Sequence: DEYEIIETIGNGAYGVVSSARRRLTGQQVAIKKIPNAFDVVTNAKRTLRELKILKHFKHDNIIAIKDILRPTVPYGEFKSVYVVLDLMESDLHQIIHSSQPLTLEHVRYFLYQLLRGLKYMHSAQVIHRDLKPSNLLVNENCELKIGDFGMARGLCTSPAEHQYFMTEYVATRWYRAPELMLSLHEYTQAIDLWSVGCIFGEMLARRQLFPGKNYVHQLQLIMMVLGTPSPAVIQAVGAERVRAYIQSLPPRQPVPWETVYPGADRQALSLLGRMLRFEPSARISAAAALRHPFLAKYHDPDDEPDCAPPFDFAFDREALTRERIKEAIVAEIEDFHARRE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1768
R free: 0.2192
Average B factor: 48
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.25
Crystallization temperature (K): 297
Crystal growth procedure: 4-6 % w/v PEG 6000, 0.1 M MES, 5 mM DTT
Matthews coefficient: 3.05
Solvent content (%): 59.63
Ligand: 3-amino-5-[(4-chlorophenyl)amino]-N-[(1S)-1-phenylethyl]-1H-1,2,4-triazole-1-carboxamide (4QZ)
Ligand formula: C17 H17 Cl N6 O
Ligand molecular weight: 356.809
Ligand SMILES: CC(c1ccccc1)NC(=O)n2c(nc(n2)N)Nc3ccc(cc3)Cl
Ligand InChI: InChI=1S/C17H17ClN6O/c1-11(12-5-3-2-4-6-12)20-17(25)24-16(22-15(19)23-24)21-14-9-7-13(18)8-10-14/h2-11H,1H3,(H,20,25)(H3,19,21,22,23)/t11-/m0/s1
Release date: 2016-05-04
RepoMan-PP1a (protein phosphatase 1, alpha isoform) holoenzyme complex (PDB entry 5IOH)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 299 residues
Sequence: GHMGSLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.566
R work: 0.1764
R free: 0.2152
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Sodium Malonate, 12% PEG 3350
Matthews coefficient: 2.05
Solvent content (%): 40.04
Release date: 2016-10-05