satarupa22/MacromolecularLigandDB huggingface dataset:
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z44567722 (PDB entry 5RWX)
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): 1.34
R work: 0.1729
R free: 0.1977
Average B factor: 18.01
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: 2.1
Solvent content (%): 41.34
Ligand: methyl 1-(tert-butylcarbamoyl)piperidine-4-carboxylate (K0V)
Ligand formula: C12 H22 N2 O3
Ligand molecular weight: 242.315
Ligand SMILES: CC(C)(C)NC(=O)N1CCC(CC1)C(=O)OC
Ligand InChI: InChI=1S/C12H22N2O3/c1-12(2,3)13-11(16)14-7-5-9(6-8-14)10(15)17-4/h9H,5-8H2,1-4H3,(H,13,16)
Release date: 2020-11-11
Mutant Human DNA Polymerase Eta R61M Inserting dCTP Opposite Template G (PDB entry 4YR3)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTMSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1759
R free: 0.219
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: NaMES (pH 6.0), polyethylene glycol monomethyl ether 2000, and calcium chloride
Matthews coefficient: 2.11
Solvent content (%): 41.65
Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
Release date: 2015-05-13
EED in complex with PRC2 allosteric inhibitor EED162 (PDB entry 5H19)
Macromolecule: Polycomb protein EED
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 367 residues
Sequence: GKKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1766
R free: 0.2154
Average B factor: 27.53
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Bis-Tris, 0.2 M MgCl2, 20% PEG 3350
Matthews coefficient: 2.24
Solvent content (%): 45.04
Ligand: 5-(furan-2-ylmethylamino)-9-(phenylmethyl)-8,10-dihydro-7H-[1,2,4]triazolo[3,4-a][2,7]naphthyridine-6-carbonitrile (LQF)
Ligand formula: C22 H20 N6 O
Ligand molecular weight: 384.434
Ligand SMILES: c1ccc(cc1)CN2CCc3c(c4nncn4c(c3C#N)NCc5ccco5)C2
Ligand InChI: InChI=1S/C22H20N6O/c23-11-19-18-8-9-27(13-16-5-2-1-3-6-16)14-20(18)22-26-25-15-28(22)21(19)24-12-17-7-4-10-29-17/h1-7,10,15,24H,8-9,12-14H2
Release date: 2017-01-25
Crystal Structure of CK2alpha with Compound 4 bound (PDB entry 5CSH)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.193
R free: 0.2067
Average B factor: 45.32
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 107mM Mes pH 6.5, 29% glycerol ethoxylate, 1 M ammonium acetate
Matthews coefficient: 2.24
Solvent content (%): 45.05
Ligand: 1-(2-chlorobiphenyl-4-yl)methanamine (54E)
Ligand formula: C13 H12 Cl N
Ligand molecular weight: 217.694
Ligand SMILES: c1ccc(cc1)c2ccc(cc2Cl)CN
Ligand InChI: InChI=1S/C13H12ClN/c14-13-8-10(9-15)6-7-12(13)11-4-2-1-3-5-11/h1-8H,9,15H2
Release date: 2016-07-27
PRMT5(M420T mutant):MEP50 complexed with inhibitor PF-06939999 (PDB entry 7MXN)
Macromolecule: Methylosome protein 50
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 366 residues
Sequence: MASHHHHHHDYDGATTENLYFQGSLRKETPPPLVPPAAREWNLPPNAPACMERQLEAARYRSDGALLLGASSLSGRCWAGSLWLFKDPCAAPNEGFCSAGVQTEAGVADLTWVGERGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDICIKVWDLAQQVVLSSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQIGCSAPGYLPTSLAWHPQQSEVFVFGDENGTVSLVDTKSTSCVLSSAVHSQCVTGLVFSPHSVPFLASLSEDCSLAVLDSSLSELFRSQAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHVVPTEPLPAPGPASVTE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.2363
R free: 0.2767
Average B factor: 78.34
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 286
Crystal growth procedure: Crystallization of full-length human PRMT5/MEP50 complexed with cofactor site inhibitors was performed at 13 degrees Celsius by hanging-drop vapor-diffusion methods.  2.5 ul of a solution of 5:1 molar ratio of inhibitor compound to PRMT5/MEP50 complex (13 mg/mL) was mixed with 2.5 ul of reservoir solution containing 13-15% (w/v) PEG3350, 0.1M MES, pH 6.5-7.5, 0.25M NaCl, and 20% (v/v) ethylene glycol.  Microseeding from initial crystals produced crystals suitable for data collection.
Matthews coefficient: 2.77
Solvent content (%): 55.55
Ligand: (1S,2S,3S,5R)-3-{[6-(difluoromethyl)-5-fluoro-1,2,3,4-tetrahydroisoquinolin-8-yl]oxy}-5-(4-methyl-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclopentane-1,2-diol (ZR1)
Ligand formula: C22 H23 F3 N4 O3
Ligand molecular weight: 448.438
Ligand SMILES: Cc1c2ccn(c2ncn1)C3CC(C(C3O)O)Oc4cc(c(c5c4CNCC5)F)C(F)F
Ligand InChI: InChI=1S/C22H23F3N4O3/c1-10-11-3-5-29(22(11)28-9-27-10)15-7-17(20(31)19(15)30)32-16-6-13(21(24)25)18(23)12-2-4-26-8-14(12)16/h3,5-6,9,15,17,19-21,26,30-31H,2,4,7-8H2,1H3/t15-,17+,19+,20-/m1/s1
Release date: 2021-11-17
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000295a (PDB entry 5QDF)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.712
R work: 0.1768
R free: 0.204
Average B factor: 34.2787
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.31
Solvent content (%): 62.89
Ligand: ~{N}2-(1~{H}-benzimidazol-2-yl)benzene-1,2-diamine (AWG)
Ligand formula: C13 H12 N4
Ligand molecular weight: 224.261
Ligand SMILES: c1ccc(c(c1)N)Nc2[nH]c3ccccc3n2
Ligand InChI: InChI=1S/C13H12N4/c14-9-5-1-2-6-10(9)15-13-16-11-7-3-4-8-12(11)17-13/h1-8H,14H2,(H2,15,16,17)
Release date: 2018-10-10
Cathepsin-K in complex with MIV-710 (PDB entry 6QLW)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 216 residues
Sequence: RAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1798
R free: 0.2252
Average B factor: 21.152
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.1
Crystallization temperature (K): 291
Crystal growth procedure: 25mM ADA pH6.1, 250mM sodium nitrate and 20% PEG 5k.mme
Matthews coefficient: 2.15
Solvent content (%): 42.68
Ligand: ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{R},6~{a}~{S})-6-chloranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-[5-fluoranyl-2-(4-methylpiperazin-1-yl)-1,3-thiazol-4-yl]benzamide (J5T)
Ligand formula: C27 H35 Cl F N5 O4 S
Ligand molecular weight: 580.114
Ligand SMILES: CC(C)CC(C(=O)N1CC(C2C1C(CO2)O)Cl)NC(=O)c3ccc(cc3)c4c(sc(n4)N5CCN(CC5)C)F
Ligand InChI: InChI=1S/C27H35ClFN5O4S/c1-15(2)12-19(26(37)34-13-18(28)23-22(34)20(35)14-38-23)30-25(36)17-6-4-16(5-7-17)21-24(29)39-27(31-21)33-10-8-32(3)9-11-33/h4-7,15,18-20,22-23,35H,8-14H2,1-3H3,(H,30,36)/t18-,19+,20+,22-,23-/m1/s1
Release date: 2020-02-19
Crystal Structure of Zn bound human Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase (PDB entry 7W9U)
Macromolecule: Isoform 5 of Focal adhesion kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 164 residues
Sequence: SSPADSYNEGVKPWRLQPQEISPPPTANLDRSNDKVYENVTGLVKAVIEMSSKIQPAPPEEYVPMVKEVGLALRTLLATVDETIPLLPASTHREIEMAQKLLNSDLGELINKMKLAQQYVMTSLQQEYKKQMLTAAHALAVDAKNLLDVIDQARLKMLGQTRPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.163
R work: 0.2148
R free: 0.275
Average B factor: 50.538
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.05 M Zinc acetate dihydrate, 20% w/v Polyethylene glycol 3,350
Matthews coefficient: 1.89
Solvent content (%): 34.97
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: 2022-12-21
Human PDE5 catalytic core in complex with avanafil (PDB entry 6L6E)
Macromolecule: cGMP-specific 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.35
Sequence length: 335 residues
Sequence: METRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQELEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.1966
R free: 0.2074
Average B factor: 31.08
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M MgSO4, 0.1M Na cacodylate pH 6.8, 18 % PEG 3350
Matthews coefficient: 2.96
Solvent content (%): 58.46
Ligand: 4-[(3-chloranyl-4-methoxy-phenyl)methylamino]-2-[(2S)-2-(hydroxymethyl)pyrrolidin-1-yl]-N-(pyrimidin-2-ylmethyl)pyrimid
ine-5-carboxamide (E6L)
Ligand formula: C23 H26 Cl N7 O3
Ligand molecular weight: 483.951
Ligand SMILES: COc1ccc(cc1Cl)CNc2c(cnc(n2)N3CCCC3CO)C(=O)NCc4ncccn4
Ligand InChI: InChI=1S/C23H26ClN7O3/c1-34-19-6-5-15(10-18(19)24)11-27-21-17(22(33)28-13-20-25-7-3-8-26-20)12-29-23(30-21)31-9-2-4-16(31)14-32/h3,5-8,10,12,16,32H,2,4,9,11,13-14H2,1H3,(H,28,33)(H,27,29,30)/t16-/m0/s1
Release date: 2020-09-02
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with PCM-0102113-001 (PDB entry 7G9A)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.583
R work: 0.2071
R free: 0.295
Average B factor: 58.99
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: 2.47
Solvent content (%): 50.11
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: 2023-07-12
Human DDAH-1, holo (Zn-bound) form (PDB entry 7USZ)
Macromolecule: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.3.18
Sequence length: 289 residues
Sequence: GPLGAAGLGHPAAFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTCCSVLINKKVDS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1508
R free: 0.1994
Average B factor: 25.4029
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM Tris-HCl (pH 8.05), 21% PEG6000
Matthews coefficient: 2.51
Solvent content (%): 50.98
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: 2022-05-11
FGFR4 complex with N-(3,5-dichloro-2-((5-((2,6-dichloro-3,5-dimethoxybenzyl)oxy)pyrimidin-2-yl)amino)phenyl)acrylamide (PDB entry 6NVG)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 300 residues
Sequence: MVSLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDRVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.20442
R free: 0.23295
Average B factor: 45.557
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 291
Crystal growth procedure: 100mM Bis-tris pH4.5, 200mM Lithium sulphate, 16% PEG 3350
Matthews coefficient: 2.74
Solvent content (%): 55.13
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: 2019-07-10
Factor Inhibiting HIF (FIH) in complex with zinc and GSK128863 (PDB entry 5OP6)
Macromolecule: Hypoxia-inducible factor 1-alpha inhibitor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.30
Sequence length: 351 residues
Sequence: SHMAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.2037
R free: 0.2274
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 300
Crystal growth procedure: 0.1M HEPES pH7.5, 1.1M ammonium sulfate, 2.5% PEG 400
Matthews coefficient: 3.37
Solvent content (%): 63.49
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: 2017-10-18
histone lysine desuccinylase Sirt5 in complex with succinyl peptide H4K91 (PDB entry 6ACP)
Macromolecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 267 residues
Sequence: PSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.20327
R free: 0.2851
Average B factor: 69.033
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M BIS-TRIS (pH 5.5), 25% w/v PEG 3350
Matthews coefficient: 2.23
Solvent content (%): 44.78
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: 2019-07-24
TTBK1 kinase domain in complex with inhibitor 29 (PDB entry 7QHW)
Macromolecule: Tau-tubulin kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 293 residues
Sequence: ADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2
R free: 0.2285
Average B factor: 68.455
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 27%  PEG 4000, 200mM NH4SO4, 100 mM Na Citrate pH5.6 and 10 mM TCEP
Matthews coefficient: 5.54
Solvent content (%): 77.78
Ligand: ~{N}-[4-(4-chloranylphenoxy)phenyl]-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine (CGI)
Ligand formula: C18 H13 Cl N4 O
Ligand molecular weight: 336.775
Ligand SMILES: c1cc(ccc1Nc2c3cc[nH]c3ncn2)Oc4ccc(cc4)Cl
Ligand InChI: InChI=1S/C18H13ClN4O/c19-12-1-5-14(6-2-12)24-15-7-3-13(4-8-15)23-18-16-9-10-20-17(16)21-11-22-18/h1-11H,(H2,20,21,22,23)
Release date: 2022-10-26
Crystal Structure of HRasG12V(GMPPNP-bound) in complex with the Ras-binding domain(RBD) of SIN1 (PDB entry 7VVG)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 166 residues
Sequence: MTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1778
R free: 0.2018
Average B factor: 31.0448
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 278
Crystal growth procedure: PEG2000
Matthews coefficient: 3.18
Solvent content (%): 62.73
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: 2022-05-18
TBK1 in complex with Inhibitor compound 35 (PDB entry 6RSU)
Macromolecule: Serine/threonine-protein kinase TBK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 663 residues
Sequence: GSGSAMGQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRVIGEDGQSVYKLTDFGAARELEDDEQFVSLYGTEEYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAATGSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEADQEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLVLEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTLLLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTKLLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLAYNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQEYTNELQET
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2893
R free: 0.3508
Average B factor: 85.74
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 294
Crystal growth procedure: 100 mM HEPES pH 7.5, 5-8% PEG 8000
Matthews coefficient: 3.26
Solvent content (%): 62.28
Ligand: 3,3,3-tris(fluoranyl)-1-[4-[(1~{R})-1-[2-[[(2~{S})-5-(5-propan-2-yloxypyrimidin-4-yl)-2,3-dihydro-1~{H}-benzimidazol-2-yl]amino]pyridin-4-yl]ethyl]piperazin-1-yl]propan-1-one (KJB)
Ligand formula: C28 H33 F3 N8 O2
Ligand molecular weight: 570.609
Ligand SMILES: CC(C)Oc1cncnc1c2ccc3c(c2)NC(N3)Nc4cc(ccn4)C(C)N5CCN(CC5)C(=O)CC(F)(F)F
Ligand InChI: InChI=1S/C28H33F3N8O2/c1-17(2)41-23-15-32-16-34-26(23)20-4-5-21-22(12-20)36-27(35-21)37-24-13-19(6-7-33-24)18(3)38-8-10-39(11-9-38)25(40)14-28(29,30)31/h4-7,12-13,15-18,27,35-36H,8-11,14H2,1-3H3,(H,33,37)/t18-,27+/m1/s1
Release date: 2020-04-01