satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of double tudor domain of human lysine demethylase KDM4A (PDB entry 5D6W)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 121 residues
Sequence: GSHMALQSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.992
R work: 0.1679
R free: 0.1955
Average B factor: 41.3238
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 293
Crystal growth procedure: Protein Solution (30mg/ml KDM4A DTD, 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.0M ammonium tartrate dibasic and 0.1M sodium acetate trihydrate pH4.6) Cryoprotected with additional 20% glycerol
Matthews coefficient: 3.72
Solvent content (%): 66.98
Ligand: S,R MESO-TARTARIC ACID (SRT)
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+
Release date: 2015-11-25
Crystal Structure of Human NADPH-Cytochrome P450 Reductase(A287P mutant) (PDB entry 5EMN)
Macromolecule: NADPH--cytochrome P450 reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.6.2.4
Sequence length: 618 residues
Sequence: GSHMVRESSFVEKMKKTGRNIIVFYGSQTGTAEEFANRLSKDAHRYGMRGMSADPEEYDLADLSSLPEIDNALVVFCMATYGEGDPTDNAQDFYDWLQETDVDLSGVKFAVFGLGNKTYEHFNAMGKYVDKRLEQLGAQRIFELGLGDDDGNLEEDFITWREQFWLAVCEHFGVEATGEESSIRQYELVVHTDIDAAKVYMGEMGRLKSYENQKPPFDAKNPFLPAVTTNRKLNQGTERHLMHLELDISDSKIRYESGDHVAVYPANDSALVNQLGKILGADLDVVMSLNNLDEESNKKHPFPCPTSYRTALTYYLDITNPPRTNVLYELAQYASEPSEQELLRKMASSSGEGKELYLSWVVEARRHILAILQDCPSLRPPIDHLCELLPRLQARYYSIASSSKVHPNSVHICAVVVEYETKAGRINKGVATNWLRAKEPVGENGGRALVPMFVRKSQFRLPFKATTPVIMVGPGTGVAPFIGFIQERAWLRQQGKEVGETLLYYGCRRSDEDYLYREELAQFHRDGALTQLNVAFSREQSHKVYVQHLLKQDREHLWKLIEGGAHIYVCGDARNMARDVQNTFYDIVAELGAMEHAQAVDYIKKLMTKGRYSLDVWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.222
R free: 0.277
Average B factor: 51.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 292
Crystal growth procedure: 100mM MES,pH6.5,50mM CaAc2,0.1M NaCl, 14% PEG4K
Matthews coefficient: 2.28
Solvent content (%): 46.09
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2016-08-17
Crystal Structure of human phosphodiesterase 10 in complex with 5-[(3R)-3-fluoropyrrolidin-1-yl]-2-(3-methylquinoxalin-2-yl)-N-(oxan-4-yl)pyrazolo[1,5-a]pyrimidin-7-amine (PDB entry 5SIX)
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: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29
R work: 0.1822
R free: 0.2189
Average B factor: 52.057
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.98
Solvent content (%): 58.72
Ligand: (8S)-5-[(3S)-3-fluoropyrrolidin-1-yl]-2-(3-methylquinoxalin-2-yl)-N-(oxan-4-yl)pyrazolo[1,5-a]pyrimidin-7-amine (JU6)
Ligand formula: C24 H26 F N7 O
Ligand molecular weight: 447.508
Ligand SMILES: Cc1c(nc2ccccc2n1)c3cc4nc(cc(n4n3)NC5CCOCC5)N6CCC(C6)F
Ligand InChI: InChI=1S/C24H26FN7O/c1-15-24(28-19-5-3-2-4-18(19)26-15)20-12-22-29-21(31-9-6-16(25)14-31)13-23(32(22)30-20)27-17-7-10-33-11-8-17/h2-5,12-13,16-17,27H,6-11,14H2,1H3
Release date: 2022-10-12
Crystal structure of hnRNP L RRM2 in complex with SETD2 (PDB entry 7EVR)
Macromolecule: Heterogeneous nuclear ribonucleoprotein L
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 111 residues
Sequence: HHHHHHMDDSRSVNSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKNGVQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKPTRLNVFKNDQDTWDYTNPN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1582
R free: 0.1979
Average B factor: 19.619
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.8M Potassium/Sodium phosphate, pH 7.5
Matthews coefficient: 2.42
Solvent content (%): 49.26
Release date: 2021-10-20
Human Carbonic Anhydrase II in complex with fragment. (PDB entry 6SB7)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 265 residues
Sequence: GSPEFMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.09
R work: 0.1183
R free: 0.1367
Average B factor: 11.43
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium sulfate 2.7 M, TRIS 0.1 M, saturated with para-Chloromercuribenzoic acid
Matthews coefficient: 2.15
Solvent content (%): 42.89
Ligand: MERCURY (II) ION (HG)
Ligand formula: Hg
Ligand molecular weight: 200.59
Ligand SMILES: [Hg+2]
Ligand InChI: InChI=1S/Hg/q+2
Release date: 2020-04-15
Crystal Structure of human Pin1 complexed with a potent covalent inhibitor (PDB entry 7F0M)
Macromolecule: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 183 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMADEEKLPPGWEKAMSRSSGRVYYFNHITNASQWERPSGNSSSGGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2152
R free: 0.2475
Average B factor: 23.7461
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 289.15
Crystal growth procedure: 30% PEG400, 100mM Tris, pH 8.0
Matthews coefficient: 2.12
Solvent content (%): 41.92
Ligand: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL (P33)
Ligand formula: C14 H30 O8
Ligand molecular weight: 326.383
Ligand SMILES: C(COCCOCCOCCOCCOCCOCCO)O
Ligand InChI: InChI=1S/C14H30O8/c15-1-3-17-5-7-19-9-11-21-13-14-22-12-10-20-8-6-18-4-2-16/h15-16H,1-14H2
Release date: 2022-02-16
Crystal structure of SMYD2 with SAM and EPZ033294 (PDB entry 5V3H)
Macromolecule: N-lysine methyltransferase SMYD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 444 residues
Sequence: SIADYKDDDDKMRAEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLGFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIESH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.69
R work: 0.2175
R free: 0.27
Average B factor: 54.016
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 5% v/v Ethanol, 0.1 M Tris pH 7.5, 26% w/v PEG3350
Matthews coefficient: 3.12
Solvent content (%): 60.52
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: 2018-04-25
MMP-13 in complex with the peptide IMISF (PDB entry 6HV2)
Macromolecule: Collagenase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24
Sequence length: 168 residues
Sequence: EYNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.709
R work: 0.2138
R free: 0.263
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 50 mM glycine, 20% PEG4000, 1 M ammonium formate, pH 9.4
Matthews coefficient: 2.35
Solvent content (%): 47.58
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: 2019-01-30
Crystal structure of human cyclophilin D (CypD) with in complex with the covalently bound Ebselen inhibitor (PDB entry 8EJX)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: SGNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1641
R free: 0.1984
Average B factor: 28.453
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 25% (w/v) PEG 4000, 100 mM Hepes, 200 NaCl
Matthews coefficient: 2
Solvent content (%): 38.65
Ligand: N-phenyl-2-selanylbenzamide (9JT)
Ligand formula: C13 H11 N O Se
Ligand molecular weight: 276.193
Ligand SMILES: c1ccc(cc1)NC(=O)c2ccccc2[SeH]
Ligand InChI: InChI=1S/C13H11NOSe/c15-13(11-8-4-5-9-12(11)16)14-10-6-2-1-3-7-10/h1-9,16H,(H,14,15)
Release date: 2023-10-18
Structure of BACE-1 in complex with Ligand 13 (PDB entry 6OD6)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 432 residues
Sequence: MHHHHHHTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGTTGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.223
R free: 0.2478
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.25
Crystallization temperature (K): 293
Crystal growth procedure: 17% PEG-4000, 0.1M MES
Matthews coefficient: 2.54
Solvent content (%): 56.15
Ligand: N-{3-[(3R)-1-amino-3-methyl-3,4-dihydropyrrolo[1,2-a]pyrazin-3-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide (M7D)
Ligand formula: C21 H17 F N6 O
Ligand molecular weight: 388.398
Ligand SMILES: CC1(Cn2cccc2C(=N1)N)c3cc(ccc3F)NC(=O)c4ccc(cn4)C#N
Ligand InChI: InChI=1S/C21H17FN6O/c1-21(12-28-8-2-3-18(28)19(24)27-21)15-9-14(5-6-16(15)22)26-20(29)17-7-4-13(10-23)11-25-17/h2-9,11H,12H2,1H3,(H2,24,27)(H,26,29)/t21-/m0/s1
Release date: 2019-09-25
CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) in complex with ferric heme and 4-Chlorophenyl imidazole (PDB entry 6E42)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 405 residues
Sequence: MGSSHHHHHHSSGSAAYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSAALELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.103
R work: 0.2026
R free: 0.2396
Average B factor: 44.0584
Crystallization method: EVAPORATION
Crystallization pH: 6.2
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M phosphate (pH 6.2), and 15% (w/v) PEG3350
Matthews coefficient: 2.44
Solvent content (%): 49.65
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2018-11-14
Glycogen Synthase Kinase 3 beta Complexed with BRD3731 (PDB entry 5KPM)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 424 residues
Sequence: GSPGMSGRPRTTSFAESCKPVQQPSAFGSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARIQAAASTPTNATAASDANTGDRGQTNNAASASASNST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.69
R work: 0.1749
R free: 0.2401
Average B factor: 63.918
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: Reservoir: 0.2 M sodium acetate, pH 7.0, 20% w/v PEG3350
Matthews coefficient: 2.96
Solvent content (%): 58.4
Ligand: (4~{S})-3-(2,2-dimethylpropyl)-4,7,7-trimethyl-4-phenyl-2,6,8,9-tetrahydropyrazolo[3,4-b]quinolin-5-one (6VM)
Ligand formula: C24 H31 N3 O
Ligand molecular weight: 377.522
Ligand SMILES: CC1(CC2=C(C(=O)C1)C(c3c([nH]nc3N2)CC(C)(C)C)(C)c4ccccc4)C
Ligand InChI: InChI=1S/C24H31N3O/c1-22(2,3)12-17-20-21(27-26-17)25-16-13-23(4,5)14-18(28)19(16)24(20,6)15-10-8-7-9-11-15/h7-11H,12-14H2,1-6H3,(H2,25,26,27)/t24-/m1/s1
Release date: 2018-03-14
CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Dasatinib (PDB entry 5VCV)
Macromolecule: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 311 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMHQLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.1555
R free: 0.1968
Average B factor: 28.4245
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000, 1 mM Dasatinib
Matthews coefficient: 2.11
Solvent content (%): 41.6
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2017-08-23
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1270087714 (PDB entry 7G8R)
Macromolecule: Rho guanine nucleotide exchange factor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 245 residues
Sequence: SMEMDEKDFAADSWSLAVDSSFLQQHKKEVMKQQDVIYELIQTELHHVRTLKIMTRLFRTGMLEELHLEPGVVQGLFPCVDELSDIHTRFLSQLLERRRQALCPGSTRNFVIHRLGDLLISQFSGPSAEQMCKTYSEFCSRHSKALKLYKELYARDKRFQQFIRKVTRPAVLKRHGVQECILLVTQRITKYPLLISRILQHSHGIEEERQDLTTALGLVKELLSNVDEGIYQLEKGARLQEIYNR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.1867
R free: 0.2073
Average B factor: 27.04
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.52
Solvent content (%): 51.15
Ligand: (2R,6S)-2,6-dimethyl-4-(3-methyl-1,2,4-thiadiazol-5-yl)morpholine (Z5Z)
Ligand formula: C9 H15 N3 O S
Ligand molecular weight: 213.3
Ligand SMILES: Cc1nc(sn1)N2CC(OC(C2)C)C
Ligand InChI: InChI=1S/C9H15N3OS/c1-6-4-12(5-7(2)13-6)9-10-8(3)11-14-9/h6-7H,4-5H2,1-3H3/t6-,7+
Release date: 2023-07-12
Human Butyrylcholinesterase complexed with N-Propargyliperidines (PDB entry 5LKR)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 574 residues
Sequence: EDDIIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNPNETQNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKVLEMTGNIDEAEWEWKAGFHRWNNYMMDWKNQFNDYTSKKESCVGL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.1855
R free: 0.2377
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M ammonium acetate, 18% PEG 4000, 20 mM Tris pH 7.4
Matthews coefficient: 2.57
Solvent content (%): 52.16
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2016-12-14
Human Erk2 with an Erk1/2 inhibitor (PDB entry 5NHP)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 381 residues
Sequence: MHHHHHHGGGENLYFQGSHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNLNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRSLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.198
R free: 0.221
Average B factor: 35.2
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 30% PegMME2K, 100mM HEPES pH 7.6, 200mM Ammonium sulfate
Matthews coefficient: 2.52
Solvent content (%): 51.1
Ligand: 5-(2-methoxyethyl)-1-methyl-2-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]-6,7-dihydropyrrolo[3,2-c]pyridin-4-one (8XK)
Ligand formula: C19 H23 N7 O2
Ligand molecular weight: 381.432
Ligand SMILES: Cn1c(ccn1)Nc2nccc(n2)c3cc4c(n3C)CCN(C4=O)CCOC
Ligand InChI: InChI=1S/C19H23N7O2/c1-24-15-6-9-26(10-11-28-3)18(27)13(15)12-16(24)14-4-7-20-19(22-14)23-17-5-8-21-25(17)2/h4-5,7-8,12H,6,9-11H2,1-3H3,(H,20,22,23)
Release date: 2017-04-19
Crystal Structure of human phosphodiesterase 10 in complex with 2-benzyl-6,6-dimethyl-1H-imidazo[4,5-h]isoquinoline-7,9-dione (PDB entry 5SI7)
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: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1905
R free: 0.2333
Average B factor: 36.742
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.63
Solvent content (%): 53.22
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: 2022-10-12
Crystal structure of IpaH1.4 LRR domain bound to HOIL-1L UBL domain. (PDB entry 7V8E)
Macromolecule: RING-type E3 ubiquitin transferase
Type: Protein, polypeptide(L)
Source organism: Shigella flexneri 5a str. M90T
EC number: 2.3.2.27
Sequence length: 240 residues
Sequence: GPGSNEFYLKTWSEWEKNGTPGEQRNIAFNRLKICLQNQEAELNLSELDLKTLPDLPPQITTLEIRKNLLTHLPDLPPMLKVIHAQFNQLESLPALPETLEELNAGDNKIKELPFLPENLTHLRVHNNRLHILPLLPPELKLLVVSGNRLDSIPPFPDKLEGLALANNFIEQLPELPFSMNRAVLMNNNLTTLPESVLRLAQNAFVNVAGNPLSGHTMRTLQQITTGPDYSGPRIFFSMG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2009
R free: 0.2457
Average B factor: 37.54
Crystallization method: EVAPORATION
Crystallization pH: 8.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.2 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.5), and 25% (w/v) PEG3350
Matthews coefficient: 2.12
Solvent content (%): 42.09
Release date: 2022-03-30
Structural basis on the interaction of Scribble PDZ domains with the Tick Born encephalitis virus (TBEV) NS5 protein (PDB entry 7QSA)
Macromolecule: Protein scribble homolog
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 92 residues
Sequence: SVEEIRLPRAGGPLGLSIVGGSDHSSHPFGVQEPGVFISKVLPRGLAARSGLRVGDRILAVNGQDVRDATHQEAVSALLRPCLELSLLVRRD
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.2527
R free: 0.2874
Average B factor: 47.71
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.2M Sodium nitrate, 0.1M Bis-Tris propane pH7.5, 20% w/v PEG 3350
Matthews coefficient: 2.32
Solvent content (%): 47.06
Release date: 2022-08-31