satarupa22/MacromolecularLigandDB huggingface dataset:
Fragment-based discovery of a highly potent, orally bioavailable inhibitor which modulates the phosphorylation and catalytic activity of ERK1/2 (PDB entry 6GE0)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.162
R free: 0.21
Average B factor: 39.662
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M (NH4)2SO4, 33.0%w/v MPEG 2000, 0.1M HEPES/NaOHpH=7.2, 0.02M Mercaptoethanol
Matthews coefficient: 2.31
Solvent content (%): 46.86
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2018-05-30
BTK in complex with an inhibitor (PDB entry 6S90)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 266 residues
Sequence: GSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.167
R free: 0.201
Average B factor: 17.47
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM Tris-HCL pH 8.5, 200 mM sodium formate, 50 mM CaCl2, 25% (w/v) PEGMME 5000
Matthews coefficient: 2.13
Solvent content (%): 42.36
Ligand: 4-~{tert}-butyl-~{N}-[2-methyl-3-[6-[4-(4-methylpiperazin-1-yl)carbonylphenyl]-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]phenyl]benzamide (L0Z)
Ligand formula: C36 H38 N6 O2
Ligand molecular weight: 586.726
Ligand SMILES: Cc1c(cccc1NC(=O)c2ccc(cc2)C(C)(C)C)c3c4cc([nH]c4ncn3)c5ccc(cc5)C(=O)N6CCN(CC6)C
Ligand InChI: InChI=1S/C36H38N6O2/c1-23-28(7-6-8-30(23)40-34(43)25-13-15-27(16-14-25)36(2,3)4)32-29-21-31(39-33(29)38-22-37-32)24-9-11-26(12-10-24)35(44)42-19-17-41(5)18-20-42/h6-16,21-22H,17-20H2,1-5H3,(H,40,43)(H,37,38,39)
Release date: 2019-09-18
Structure of J-PKAc chimera complexed with Aplithianine B (PDB entry 8FE5)
Macromolecule: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.11
Sequence length: 405 residues
Sequence: GKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKREIFDRYGEEVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.1901
R free: 0.2432
Average B factor: 58.08
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 200 mM Lithium Sulfate, 100 mM HEPES 7.5, 25% PEG 3350
Matthews coefficient: 2.71
Solvent content (%): 54.64
Ligand: 6-[(6P)-6-(1-methyl-1H-imidazol-5-yl)-2,3-dihydro-4H-1,4-thiazin-4-yl]-7,9-dihydro-8H-purin-8-one (XTT)
Ligand formula: C13 H13 N7 O S
Ligand molecular weight: 315.354
Ligand SMILES: Cn1cncc1C2=CN(CCS2)c3c4c(ncn3)NC(=O)N4
Ligand InChI: InChI=1S/C13H13N7OS/c1-19-7-14-4-8(19)9-5-20(2-3-22-9)12-10-11(15-6-16-12)18-13(21)17-10/h4-7H,2-3H2,1H3,(H2,15,16,17,18,21)
Release date: 2023-10-18
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z57299529 (PDB entry 5RWZ)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.42
R work: 0.1709
R free: 0.1968
Average B factor: 19.115
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.09
Solvent content (%): 41.24
Ligand: N-[(Z)-2-phenylethenyl]-1H-benzimidazol-2-amine (WNG)
Ligand formula: C15 H13 N3
Ligand molecular weight: 235.284
Ligand SMILES: c1ccc(cc1)C=CNc2[nH]c3ccccc3n2
Ligand InChI: InChI=1S/C15H13N3/c1-2-6-12(7-3-1)10-11-16-15-17-13-8-4-5-9-14(13)18-15/h1-11H,(H2,16,17,18)/b11-10-
Release date: 2020-11-11
Crystal Structure of EGFR-T790M/C797S in Complex with Brigatinib (PDB entry 7ZYM)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 333 residues
Sequence: GSHMASGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGSLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1923
R free: 0.2237
Average B factor: 70.43
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.4 K-Na-tartrate, 100 mM Na-MES (pH 6.5),
3.5 mg/mL EGFR-WT (in 100 mM NaCl, 25 mM Tris-HCl, 10 % glycerol, 1 mM TCEP) pH 8.0) 1 ul reservoir + 1 ul solution
Matthews coefficient: 3.45
Solvent content (%): 64.3
Ligand: 5-chloro-N~4~-[2-(dimethylphosphoryl)phenyl]-N~2~-{2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl}pyrimidine-2,4-diamine (6GY)
Ligand formula: C29 H39 Cl N7 O2 P
Ligand molecular weight: 584.092
Ligand SMILES: CN1CCN(CC1)C2CCN(CC2)c3ccc(c(c3)OC)Nc4ncc(c(n4)Nc5ccccc5P(=O)(C)C)Cl
Ligand InChI: InChI=1S/C29H39ClN7O2P/c1-35-15-17-37(18-16-35)21-11-13-36(14-12-21)22-9-10-24(26(19-22)39-2)33-29-31-20-23(30)28(34-29)32-25-7-5-6-8-27(25)40(3,4)38/h5-10,19-21H,11-18H2,1-4H3,(H2,31,32,33,34)
Release date: 2023-05-03
Hect domain of AREL1 (PDB entry 6JX5)
Macromolecule: Apoptosis-resistant E3 ubiquitin protein ligase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 388 residues
Sequence: SETFQDKVNFFQRELRQVHMKRPHSKVTLKVSRHALLESSLKATRNFSISDWSKNFEVVFQDEEALDWGGPRREWFELICKALFDTTNQLFTRFSDNNQALVHPNPNRPAHLRLKMYEFAGRLVGKCLYESSLGGAYKQLVRARFTRSFLAQIIGLRMHYKYFETDDPEFYKSKVCFILNNDMSEMELVFAEEKYNKSGQLDKVVELMTGGAQTPVTNANKIFYLNLLAQYRLASQVKEEVEHFLKGLNELVPENLLAIFDENELELLMCGTGDISVSDFKAHAVVVGGSWHFREKVMRWFWTVVSSLTQEELARLLQFTTGSSQLPPGGFAALCPSFQIIAAPTHSTLPTAHTCFNQLCLPTYDSYEEVHRMLQLAISEGCEGFGML
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.402
R work: 0.1857
R free: 0.2181
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 296.15
Crystal growth procedure: 100mM Bis Tris (pH 5.5), 200mM Ammonium sulfate
Matthews coefficient: 3.93
Solvent content (%): 68.74
Release date: 2019-12-04
ERK5 IN COMPLEX WITH SMALL MOLECULE (PDB entry 5BYY)
Macromolecule: Mitogen-activated protein kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 346 residues
Sequence: FDVGDEYEIIETIGNGAYGVVSSARRRLTGQQVAIKKIPNAFDVVTNAKRTLRELKILKHFKHDNIIAIKDILRPTVPYGEFKSVYVVLDLMESDLHQIIHSSQPLTLEHVRYFLYQLLRGLKYMHSAQVIHRDLKPSNLLVNENCELKIGDFGMARGLCTSPAEHQYFMTEYVATRWYRAPELMLSLHEYTQAIDLWSVGCIFGEMLARRQLFPGKNYVHQLQLIMMVLGTPSPAVIQAVGAERVRAYIQSLPPRQPVPWETVYPGADRQALSLLGRMLRFEPSARISAAAALRHPFLAKYHDPDDEPDCAPPFDFAFDREALTRERIKEAIVAEIEDFHARREG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.79
R work: 0.22059
R free: 0.27285
Average B factor: 19.315
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.01 M Tris 8.50
0.01 M MgCl2
13 % PEG4000
0.18 M Na-formiate
0.10 M MES, pH=6.50
Matthews coefficient: 2.97
Solvent content (%): 58.58
Ligand: 2-{[2-ethoxy-4-(4-hydroxypiperidin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one (4WG)
Ligand formula: C26 H30 N6 O3
Ligand molecular weight: 474.555
Ligand SMILES: CCOc1cc(ccc1Nc2ncc3c(n2)N(c4ccccc4C(=O)N3C)C)N5CCC(CC5)O
Ligand InChI: InChI=1S/C26H30N6O3/c1-4-35-23-15-17(32-13-11-18(33)12-14-32)9-10-20(23)28-26-27-16-22-24(29-26)30(2)21-8-6-5-7-19(21)25(34)31(22)3/h5-10,15-16,18,33H,4,11-14H2,1-3H3,(H,27,28,29)
Release date: 2016-05-04
Crystal structure of CK2 with compound 7h (PDB entry 5H8E)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 333 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1648
R free: 0.1961
Average B factor: 32.01
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 22-26% PEG 6K, 200 mM ammonium sulfate, 100 mM MES, pH 6.5
Matthews coefficient: 3.14
Solvent content (%): 60.89
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2016-02-10
X-ray structure of NSD3-PWWP1 in complex with compound 4 (PDB entry 6G25)
Macromolecule: Histone-lysine N-methyltransferase NSD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 136 residues
Sequence: STGVKFQVGDLVWSKVGTYPWWPCMVSSDPQLEVHTKINTRGAREYHVQFFSNQPERAWVHEKRVREYKGHKQYEELLAEATKQASNHSEKQKIRKPRPQRERAQWDIGIAHAEKALKMTREERIEQYTFIYIDKQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.432
R work: 0.206
R free: 0.229
Average B factor: 33.69
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols
Matthews coefficient: 2.3
Solvent content (%): 46.59
Ligand: 3,5-dimethyl-4-(4-pyridin-4-yl-1~{H}-pyrazol-3-yl)-1,2-oxazole (EHQ)
Ligand formula: C13 H12 N4 O
Ligand molecular weight: 240.261
Ligand SMILES: Cc1c(c(on1)C)c2c(c[nH]n2)c3ccncc3
Ligand InChI: InChI=1S/C13H12N4O/c1-8-12(9(2)18-17-8)13-11(7-15-16-13)10-3-5-14-6-4-10/h3-7H,1-2H3,(H,15,16)
Release date: 2019-06-26
Crystal Structure of the Human vaccinia-related kinase bound to BI-D1870 (PDB entry 5UVF)
Macromolecule: Serine/threonine-protein kinase VRK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.173
R free: 0.204
Average B factor: 52.86
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG3350, 0.1M BISTRIS, 0.2M,  LITHIUM SULFATE, PH 6.5
Matthews coefficient: 2.56
Solvent content (%): 51.96
Ligand: (7S)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8-dihydropteridin-6(5H)-one (7DZ)
Ligand formula: C19 H23 F2 N5 O2
Ligand molecular weight: 391.415
Ligand SMILES: CC1C(=O)N(c2cnc(nc2N1CCC(C)C)Nc3cc(c(c(c3)F)O)F)C
Ligand InChI: InChI=1S/C19H23F2N5O2/c1-10(2)5-6-26-11(3)18(28)25(4)15-9-22-19(24-17(15)26)23-12-7-13(20)16(27)14(21)8-12/h7-11,27H,5-6H2,1-4H3,(H,22,23,24)/t11-/m0/s1
Release date: 2017-03-22
Crystal structure of human CK2a with AMPPNP (PDB entry 3WOW)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 340 residues
Sequence: GPLGSMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.18448
R free: 0.23964
Average B factor: 31.914
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 25% ethylene glycol, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Matthews coefficient: 1.93
Solvent content (%): 36.14
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: 2015-02-04
Crystal Structure of Human Methyltransferase-like protein 13 in complex with SAH (PDB entry 5WCJ)
Macromolecule: Methyltransferase-like protein 13
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 248 residues
Sequence: MHHHHHHSSGRENLYFQGCCEHHKAMIAGLALLRNPELLLEIPLALLVVGLGGGSLPLFVHDHFPKSCIDAVEIDPSMLEVATQWFGFSQSDRMKVHIADGLDYIASLAGGGEARPCYDVIMFDVDSKDPTLGMSCPPPAFVEQSFLQKVKSILTPEGVFILNLVCRDLGLKDSVLAGLKAVFPLLYVRRIEGEVNEILFCQLHPEQKLATPELLETAQALERTLRKPGRGWDDTYVLSDMLKTVKIV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1869
R free: 0.2125
Average B factor: 35.246
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG3350, 200mM Ammonium Chloride
Matthews coefficient: 2.19
Solvent content (%): 43.74
Ligand: UNKNOWN ATOM OR ION (UNX)
Ligand formula: X
Ligand SMILES: *
Release date: 2017-07-19
Crystal Structure of human phosphodiesterase 10 in complex with N-(2-chloropyridin-4-yl)-2-phenylpyrazolo[1,5-a]pyridine-6-carboxamide (PDB entry 5SFP)
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
R work: 0.1869
R free: 0.2256
Average B factor: 33.747
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: 2.64
Solvent content (%): 53.48
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2022-10-12
CRYSTAL STRUCTURE OF INACTIVE KRAS G12D (GDP) IN COMPLEX WITH THE SOAKED DIMERIC INHIBITOR BI-5747 (PDB entry 7ACQ)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Homo 3-mer
Stoichiometry: A3
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1737
R free: 0.2097
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 278
Crystal growth procedure: 200 mM CaCl2
100 mM MES pH6
PEG6000 20% W/v
Matthews coefficient: 2.38
Solvent content (%): 48.38
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2020-11-18
Human Cyclophilin D Complexed with Inhibitor (PDB entry 5CBT)
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: MGNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.17749
R free: 0.19856
Average B factor: 16.785
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 291
Crystal growth procedure: 4M potassium formate, 0.1M BIS-TRIS propane pH 9, 2% w/v PEG2000mme
Matthews coefficient: 2.69
Solvent content (%): 54.31
Ligand: ethyl N-(benzylcarbamoyl)glycinate (4ZL)
Ligand formula: C12 H16 N2 O3
Ligand molecular weight: 236.267
Ligand SMILES: CCOC(=O)CNC(=O)NCc1ccccc1
Ligand InChI: InChI=1S/C12H16N2O3/c1-2-17-11(15)9-14-12(16)13-8-10-6-4-3-5-7-10/h3-7H,2,8-9H2,1H3,(H2,13,14,16)
Release date: 2016-07-20
Crystal structure of CLK1 in complex with inhibitor 8g (PDB entry 6FT8)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 339 residues
Sequence: SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.16411
R free: 0.19533
Average B factor: 26.987
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 20% PEG3350, 0.1 M sodium malonate
Matthews coefficient: 2.6
Solvent content (%): 52.68
Ligand: 3-(3-hydroxyphenyl)-1~{H}-pyrrolo[3,4-g]indol-8-one (E6T)
Ligand formula: C16 H10 N2 O2
Ligand molecular weight: 262.263
Ligand SMILES: c1cc(cc(c1)O)c2c[nH]c3c2ccc4c3C(=O)N=C4
Ligand InChI: InChI=1S/C16H10N2O2/c19-11-3-1-2-9(6-11)13-8-17-15-12(13)5-4-10-7-18-16(20)14(10)15/h1-8,17,19H
Release date: 2018-05-16
Structure of CaMKK2 in complex with CKI-002 (PDB entry 5YV8)
Macromolecule: Calcium/calmodulin-dependent protein kinase kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 298 residues
Sequence: GSSGSSGDCVQLNQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAGFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNTVGTPAFMAPESLSETRKIFSGKALDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.927
R work: 0.1637
R free: 0.2126
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M sodium cacodylate (pH 6.0), 0.2M Sodium acetate, 22% PEG 8000, 0.03M glycyl-glycyl-glycine
Matthews coefficient: 3.19
Solvent content (%): 61.49
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: 2018-12-05
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z1478435544 (PDB entry 5RWS)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.28
R work: 0.1739
R free: 0.1935
Average B factor: 16.115
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.11
Solvent content (%): 41.6
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2020-11-11