satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the KDR (VEGFR2) kinase domain in complex with a type-II inhibitor bearing an acrylamide (PDB entry 6XVK)
Macromolecule: Vascular endothelial growth factor receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 322 residues
Sequence: MDPDELPLDEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANAQQDENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.206
R free: 0.244
Average B factor: 75.99
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 11 % PEG8000, 0.1 M PCTP buffer pH 6.5
Matthews coefficient: 2.24
Solvent content (%): 45.08
Ligand: ~{N}-(4,4-dimethyl-2-prop-1-ynyl-3,1-benzoxazin-6-yl)-2-[3-methoxy-5-(7-methoxyquinolin-4-yl)oxy-pyridin-2-yl]ethanamide (O3E)
Ligand formula: C31 H28 N4 O5
Ligand molecular weight: 536.578
Ligand SMILES: CC#CC1=Nc2ccc(cc2C(O1)(C)C)NC(=O)Cc3c(cc(cn3)Oc4ccnc5c4ccc(c5)OC)OC
Ligand InChI: InChI=1S/C31H28N4O5/c1-6-7-30-35-24-11-8-19(14-23(24)31(2,3)40-30)34-29(36)17-26-28(38-5)16-21(18-33-26)39-27-12-13-32-25-15-20(37-4)9-10-22(25)27/h8-16,18H,17H2,1-5H3,(H,34,36)
Release date: 2020-05-27
Crystal structure of cyclophilin D in complex with CsA analogue, JW47. (PDB entry 5A0E)
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: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.09806
R free: 0.13122
Average B factor: 15.02
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 2.9
Crystal growth procedure: HANGING DROP 50:50. PRECIPITANT: 23% POLYETHYLENE GLYCOL (PEG3350), 50 MM SODIUM-CITRATE BUFFER AT PH 2.9 PROTEIN: 30 MG/ML IN 50MM POTASSIUM/SODIUM PHOSPHATE PH 7.3, 100MM NACL, 2MM EDTA, 0.02% SODIUM AZIDE.
Matthews coefficient: 2.04
Solvent content (%): 39.6
Release date: 2015-12-30
Crystal structure of JAK2 JH2-V617F in complex with Z902-A3 (PDB entry 8B9E)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCFCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAWAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1689
R free: 0.1938
Average B factor: 31.55
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Tris pH 8, 20% PEG4000, 0.2M Na-acetate
Matthews coefficient: 2.61
Solvent content (%): 52.88
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: 2023-02-01
Bruton's tyrosine kinase in complex with compound 45 (PDB entry 7N4Q)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 269 residues
Sequence: GYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1886
R free: 0.2201
Average B factor: 24.59
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M BisTRIS pH 6.5, 0.2M Ammonium Acetate, 0.1M Guanidine HCl, 20% PEG2200 MME
Matthews coefficient: 2.29
Solvent content (%): 46.4
Ligand: (2R)-2-(3-chloro-5-fluoroanilino)-2-cyclopropyl-N-[(3R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]acetamide (0B9)
Ligand formula: C22 H24 Cl F N6 O
Ligand molecular weight: 442.917
Ligand SMILES: c1c[nH]c2c1c(ncn2)N3CCCC(C3)NC(=O)C(C4CC4)Nc5cc(cc(c5)Cl)F
Ligand InChI: InChI=1S/C22H24ClFN6O/c23-14-8-15(24)10-17(9-14)28-19(13-3-4-13)22(31)29-16-2-1-7-30(11-16)21-18-5-6-25-20(18)26-12-27-21/h5-6,8-10,12-13,16,19,28H,1-4,7,11H2,(H,29,31)(H,25,26,27)/t16-,19-/m1/s1
Release date: 2022-05-18
MerTK kinase domain in complex with quinazoline-based inhbitor (PDB entry 7AVY)
Macromolecule: Tyrosine-protein kinase Mer
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 296 residues
Sequence: GSEELQNKLEDVVIDRNLLILGKILGEGEFGSVMEGNLKQEDGTSLKVAVKTMKLDNSSQREIEEFLSEAACMKDFSHPNVIRLLGVCIEMSSQGIPKPMVILPFMKYGDLHTYLLYSRLETGPKHIPLQTLLKFMVDIALGMEYLSNRNFLHRDLAARNCMLRDDMTVCVADFGLSKKIYSGDYYRQGRIAKMPVKWIAIESLADRVYTSKSDVWAFGVTMWEIATRGMTPYPGVQNHEMYDYLLHGHRLKQPEDCLDELYEIMYSCWRTDPLDRPTFSVLRLQLEKLLESLPDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.31
R work: 0.228
R free: 0.249
Average B factor: 99.07
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: co-crystallisation of 0.3 mM protein with 0.5 mM compound (1 % DMSO) in 1.8 M lithium sulfate, 0.1 M PCTP pH 6.5
Matthews coefficient: 3.58
Solvent content (%): 65.62
Ligand: N-(2-(2-cyclopropylethoxy)pyrimidin-5-yl)-7-methoxy-6-(piperidin-4-ylmethoxy)quinazolin-4-amine (S4E)
Ligand formula: C24 H30 N6 O3
Ligand molecular weight: 450.533
Ligand SMILES: COc1cc2c(cc1OCC3CCNCC3)c(ncn2)Nc4cnc(nc4)OCCC5CC5
Ligand InChI: InChI=1S/C24H30N6O3/c1-31-21-11-20-19(10-22(21)33-14-17-4-7-25-8-5-17)23(29-15-28-20)30-18-12-26-24(27-13-18)32-9-6-16-2-3-16/h10-13,15-17,25H,2-9,14H2,1H3,(H,28,29,30)
Release date: 2021-03-03
Crystal structure of human ATAD2 bromodomain in complex with 3-methyl- 8-piperidin-4-ylamino-1,2-dihydro-1,7-naphthyridin-2-one hydrochloride (PDB entry 5A5Q)
Macromolecule: ATPASE FAMILY AAA DOMAIN-CONTAINING PROTEIN 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.22145
R free: 0.25244
Average B factor: 26.392
Crystal growth procedure: 0.1M TRISHCL PH 7.0-8.0, 1.2-1.5M AMMONIUM SULPHATE,20-25% PEG3350
Matthews coefficient: 4.08
Solvent content (%): 69.83
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2015-07-22
Tsetse thrombin inhibitor in complex with human alpha-thrombin - orthorhombic form at 7keV (PDB entry 6TKH)
Macromolecule: Thrombin light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1606
R free: 0.2003
Average B factor: 37.11
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate, 25 % (w/v) PEG 3350
Matthews coefficient: 2.33
Solvent content (%): 47.3
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: 2020-11-04
Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 in unliganded form (PDB entry 7JHK)
Macromolecule: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.149
Sequence length: 370 residues
Sequence: MHHHHHHHHENLYFQGSKEKFWKISTPPEAYWNREQEKLNRQYNPILSMLTNQTGEAGRLSNISHLNYCEPDLRVTSVVTGFNNLPDRFKDFLLYLRCRNYSLLIDQPDKCAKKPFLLLAIKSLTPHFARRQAIRESWGQESNAGNQTVVRVFLLGQTPPEDNHPDLSDMLKFESEKHQDILMWNYRDTFFNLSLKEVLFLRWVSTSCPDTEFVFKGDDDVFVNTHHILNYLNSLSKTKAKDLFIGDVIHNAGPHRDKKLKYYIPEVVYSGLYPPYAGGGGFLYSGHLALRLYHITDQVHLYPIDDVYTGMCLQKLGLVPEKHKGFRTFDIEEKNKNNICSYVDLMLVHSRKPQEMIDIWSQLQSAHLKC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3436
R work: 0.1792
R free: 0.2173
Average B factor: 37.6384
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 24% PEG1500, 20% glycerol
Matthews coefficient: 2.43
Solvent content (%): 49.32
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: 2020-11-18
Crystal structure of BRAF:MEK1 complex (PDB entry 6PP9)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 283 residues
Sequence: GGGRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.59
R work: 0.2207
R free: 0.2455
Average B factor: 53.5009
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Bis-Tris pH 6.4, 200 mM Ammonium Sulfate, and 22% PEG3350
Matthews coefficient: 3.39
Solvent content (%): 67.29
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2019-10-09
BACE1 in complex with 4-(cyclohexylamino)-1-(3-fluorophenyl)-8-(3-isopropoxybenzyl)-1,3,8-triazaspiro[4.5]dec-3-en-2-one (PDB entry 4ZPE)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 405 residues
Sequence: MLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGAWAGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1879
R free: 0.2041
Average B factor: 30.4007
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.5M LITHIUM SULFATE, 0.1M HEPES BUFFER PH 7.50
Matthews coefficient: 3.11
Solvent content (%): 60.44
Ligand: 4-(cyclohexylamino)-1-(3-fluorophenyl)-8-[3-(propan-2-yloxy)benzyl]-1,3,8-triazaspiro[4.5]dec-3-en-2-one (4QA)
Ligand formula: C29 H37 F N4 O2
Ligand molecular weight: 492.628
Ligand SMILES: CC(C)Oc1cccc(c1)CN2CCC3(CC2)C(=NC(=O)N3c4cccc(c4)F)NC5CCCCC5
Ligand InChI: InChI=1S/C29H37FN4O2/c1-21(2)36-26-13-6-8-22(18-26)20-33-16-14-29(15-17-33)27(31-24-10-4-3-5-11-24)32-28(35)34(29)25-12-7-9-23(30)19-25/h6-9,12-13,18-19,21,24H,3-5,10-11,14-17,20H2,1-2H3,(H,31,32,35)
Release date: 2015-08-05
The structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with JES107 (PDB entry 5NEI)
Macromolecule: Serine/threonine-protein kinase PLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.21
Sequence length: 237 residues
Sequence: GAHMDCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSRSASNRLKAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.1987
R free: 0.2476
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 292
Crystal growth procedure: 10% PEG 3350, 100 mM Na/K tartrate
Matthews coefficient: 1.98
Solvent content (%): 37.81
Ligand: 2-[[3-[[5-(3-iodanylphenyl)carbonylthiophen-2-yl]carbonylamino]phenyl]methyl]propanedioic acid (8VB)
Ligand formula: C22 H16 I N O6 S
Ligand molecular weight: 549.335
Ligand SMILES: c1cc(cc(c1)NC(=O)c2ccc(s2)C(=O)c3cccc(c3)I)CC(C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C22H16INO6S/c23-14-5-2-4-13(11-14)19(25)17-7-8-18(31-17)20(26)24-15-6-1-3-12(9-15)10-16(21(27)28)22(29)30/h1-9,11,16H,10H2,(H,24,26)(H,27,28)(H,29,30)
Release date: 2018-02-21
Tricomplex of RMC-7977, KRAS G12A, and CypA (PDB entry 8TBJ)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: SMTEYKLVVVGAAGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1853
R free: 0.2155
Average B factor: 24.95
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 24% PEG4000, 0.1 M Tris-HCl, pH 8.0
Matthews coefficient: 2.27
Solvent content (%): 45.9
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2024-02-07
The X-RAY co-crystal structure of human FGFR3 and KIN-3248 (PDB entry 8UDT)
Macromolecule: Fibroblast growth factor receptor 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 297 residues
Sequence: MSELELPADPKWELSRARLTLGKPLGEGCFGQVVMAEAIGIDKDRAAKPVTVAVKMLKDDATDKDLSDLVSEMEMMKMIGKHKNIINLLGACTQGGPLYVLVEYAAKGNLREFLRARRSGEEQLTFKDLVSCAYQVARGMEYLASQKCIHRDLAARNVLVTEDNVMKIADFGLARDVHNLDYYKKTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLLWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTHDLYMIMRECWHAAPSQRPTFKQLVEDLDRVLTVTSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.829
R work: 0.2623
R free: 0.274
Average B factor: 107.42
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.20 M DL-Malic acid pH 5.00,
18.00 % (w/v) PEG 4000
Matthews coefficient: 3.19
Solvent content (%): 61.49
Ligand: D-MALATE (MLT)
Ligand formula: C4 H6 O5
Ligand molecular weight: 134.087
Ligand SMILES: C(C(C(=O)O)O)C(=O)O
Ligand InChI: InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m1/s1
Release date: 2024-02-07
CCP5 in complex with Glu-P-peptide 2 transition state analog (PDB entry 8V3P)
Macromolecule: Cytosolic carboxypeptidase-like protein 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17
Sequence length: 524 residues
Sequence: NELRCGGLLFSSRFDSGNLAHVEKVESLSSDGEGVGGGASALTSGIASSPDYEFNVWTRPDCAETEFENGNRSWFYFSVRGGMPGKLIKINIMNMNKQSKLYSQGMAPFVRTLPTRPRWERIRDRPTFEMTETQFVLSFVHRFVEGRGATTFFAFCYPFSYSDCQELLNQLDQRFPENHPTHSSPLDTIYYHRELLCYSLDGLRVDLLTITSCHGLREDREPRLEQLFPDTSTPRPFRFAGKRIFFLSSRVHPGETPSSFVFNGFLDFILRPDDPRAQTLRRLFVFKLIPMLNPDGVVRGHYRTDSRGVNLNRQYLKPDAVLHPAIYGAKAVLLYHHVSGSGGSGVAYYVDLHGHASKRGCFMYGNSFSDESTQVENMLYPKLISLNSAHFDFQGCNFSEKNMYARDRRDGQSKEGSGRVAIYKASGIIHSYTLACNYNTGRSVNSIPAACHDNGRASPPPPPAFPSRYTVELFEQVGRAMAIAALDMAECNPWPRIVLSEHSSLTNLRAWMLKHVRNSRGLSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.2146
R free: 0.2253
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 0.15 M DL-Malic acid, pH7.0, 0.1 M imidazole, pH7.0, 16% PEG MME 550
Matthews coefficient: 2.23
Solvent content (%): 44.8
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: 2024-07-17
Crystal structure of the pleckstrin-homology domain of Bcr-Abl in complex with monobody Mb(Bcr-PH_4). (PDB entry 5OC7)
Macromolecule: Breakpoint cluster region protein,pleckstrin-homology domain of Bcr-Abl
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 133 residues
Sequence: GAMGEHRQLLKDSFMVELVEGARKLRHVFLFTDLLLCTKLKKQSGGKTQQYDCKWYIPLTDLSFQMVDEPSMAFRVHSRNGKSYTFLISSDYERAEWRENIREQQKKCFRSFSLTSVELQMLTNSCVKLQTVH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.652
R work: 0.1742
R free: 0.2043
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Potassium thiocyanate, 30% (w/v) PEG MME 2000
Matthews coefficient: 2.47
Solvent content (%): 50
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: 2017-12-27
PRMT5/MEP50 crystal structure with MTA and a phthalazinone inhibitor bound (compound (M)-31) (PDB entry 7S1R)
Macromolecule: Protein arginine N-methyltransferase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.320
Sequence length: 645 residues
Sequence: MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1794
R free: 0.2225
Average B factor: 50.53
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 281
Crystal growth procedure: 100 mM Sodium Citrate pH 5, 9% PEG 4000, 150 mM Sodium Acetate
Matthews coefficient: 2.87
Solvent content (%): 57.13
Ligand: 5'-DEOXY-5'-METHYLTHIOADENOSINE (MTA)
Ligand formula: C11 H15 N5 O3 S
Ligand molecular weight: 297.334
Ligand SMILES: CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
Release date: 2022-01-26
Human alkaline sphingomyelinase (alk-SMase, ENPP7, NPP7) (PDB entry 5UDY)
Macromolecule: Ectonucleotide pyrophosphatase/phosphodiesterase family member 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.12
Sequence length: 422 residues
Sequence: DRHHHHHHKLAPVQSQGSQNKLLLVSFDGFRWNYDQDVDTPNLDAMARDGVKARYMTPAFVTMTSPCHFTLVTGKYIENHGVVHNMYYNTTSKVKLPYHATLGIQRWWDNGSVPIWITAQRQGLRAGSFFYPGGNVTYQGVAVTRSRKEGIAHNYKNETEWRANIDTVMAWFTEEDLDLVTLYFGEPDSTGHRYGPESPERREMVRQVDRTVGYLRESIARNHLTDRLNLIITSDHGMTTVDKRAGDLVEFHKFPNFTFRDIEFELLDYGPNGMLLPKEGRLEKVYDALKDAHPKLHVYKKEAFPEAFHYANNPRVTPLLMYSDLGYVIHGRINVQFNNGEHGFDNKDMDMKTIFRAVGPSFRAGLEVEPFESVHVYELMCRLLGIVPEANDGHLATLLPMLHTESALPPDGRPTLLPKGRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1788
R free: 0.207
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: sodium iodide, PEG 3350
Matthews coefficient: 3.61
Solvent content (%): 65.94
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2017-03-22
LTA4 hydrolase in complex with compound LYS006 (PDB entry 7AUZ)
Macromolecule: Leukotriene A-4 hydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 613 residues
Sequence: GPGPEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPDVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1707
R free: 0.2055
Average B factor: 25.27
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 8000, 0.1 IMIDAZOLE PH 6.8, 0.1 SODIUM ACETATE, 0.005 M YBCL3
Matthews coefficient: 2.42
Solvent content (%): 49.07
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: 2021-02-17
Crystal Structure of human phosphodiesterase 10 in complex with 4-(azetidine-1-carbonyl)-2-methyl-N-[2-(5-phenyl-2-pyridin-2-yl-1,2,4-triazol-3-yl)ethyl]pyrazole-3-carboxamide (PDB entry 5SF8)
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): 2.15
R work: 0.1712
R free: 0.2254
Average B factor: 41.426
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 (%): 53.16
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