satarupa22/MacromolecularLigandDB huggingface dataset:
Human cathepsin K mutant C25S (PDB entry 5JH3)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 223 residues
Sequence: YIPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSSWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1869
R free: 0.2113
Average B factor: 26.3967
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M ammonium sulfate, 30% (w/v) PEG-8000
Matthews coefficient: 2.24
Solvent content (%): 45.15
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: 2016-11-30
Crystal structure of MAP2K7 complexed with a covalent inhibitor 12 (PDB entry 7CBX)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 323 residues
Sequence: TGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTSAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGISGRLVDSKAKTRSAGCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTESPRTSGVLSQPHLPFFRHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.061
R work: 0.1816
R free: 0.2236
Average B factor: 40.38
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG3350
Matthews coefficient: 2.46
Solvent content (%): 50
Ligand: 3-(1H-indazol-3-yl)-5-(prop-2-enoylamino)-N-prop-2-ynyl-benzamide (FU6)
Ligand formula: C20 H16 N4 O2
Ligand molecular weight: 344.367
Ligand SMILES: C=CC(=O)Nc1cc(cc(c1)C(=O)NCC#C)c2c3ccccc3[nH]n2
Ligand InChI: InChI=1S/C20H16N4O2/c1-3-9-21-20(26)14-10-13(11-15(12-14)22-18(25)4-2)19-16-7-5-6-8-17(16)23-24-19/h1,4-8,10-12H,2,9H2,(H,21,26)(H,22,25)(H,23,24)
Release date: 2020-09-30
Crystal Structure of human phosphodiesterase 10 (PDB entry 5SJH)
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: 0.1774
R free: 0.2036
Average B factor: 41.92
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: 2.68
Solvent content (%): 54.12
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
EphA2 LBD in complex with bA-WLA-Yam peptide (PDB entry 6NK0)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 187 residues
Sequence: MASQGPGEVVLLDFAAAGGELGWLTHPYGKGWDLMQNIMNDMPIYMYSVCNVMSGDQDNWLRTNWVYRGEAERIFIELKFTVRDCNSFPGGASSCKETFNLYYAESDLDYGTNFQKRLFTKIDTIAPDEITVSSDFEARHVKLNVEERSVGPLTRKGFYLAFQDIGACVALLSVRVYYKKAHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.1512
R free: 0.1771
Average B factor: 24.6
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.09M BIS-TRIS pH5.5, 22.5% w/v PEG 3,350, 3% w/v 6-aminohexanoic acid
Matthews coefficient: 2.33
Solvent content (%): 47.17
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: 2019-05-01
Crystal structure of the EphA2 intracellular KD-SAM domains (PDB entry 7KJA)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 390 residues
Sequence: GPGDPHTYEDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSGSEGVPFRTVSEWLESIKMQQYTEHFMAAGYTAIEKVVQMTNDDIKRIGVRLPGHQKRIAYSLLGLKDQVNTVGIPI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1884
R free: 0.2175
Average B factor: 33.04
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 287
Crystal growth procedure: 0.2 M MgCl2, 0.1 M Bis-Tris pH5.5, 25% PEG 3350
Matthews coefficient: 2.6
Solvent content (%): 52.74
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: 2021-02-03
Crystal structure of USP7 catalytic domain [L299A] mutant in complex with ubiquitin (PDB entry 5KYF)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 351 residues
Sequence: GSHMKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQEACRVLLDNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1757
R free: 0.1852
Average B factor: 20.989
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1M HEPES pH 7.5, 25% PEG3350
Matthews coefficient: 2.15
Solvent content (%): 42.85
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: 2017-08-09
BACE crystal structure with hydroxy pyrrolidine inhibitor (PDB entry 6BFX)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 442 residues
Sequence: MAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.198
R free: 0.233
Average B factor: 25.95
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 17% PEG 8000, 0.2M ammonium sulfate, 0.1M sodium cacodylate
Matthews coefficient: 2.65
Solvent content (%): 53.5
Ligand: N-{(1S,2S)-3-(3,5-difluorophenyl)-1-[(3R,5S,6R)-6-(2,2-dimethylpropoxy)-5-methylmorpholin-3-yl]-1-hydroxypropan-2-yl}acetamide (DKJ)
Ligand formula: C21 H32 F2 N2 O4
Ligand molecular weight: 414.487
Ligand SMILES: CC1C(OCC(N1)C(C(Cc2cc(cc(c2)F)F)NC(=O)C)O)OCC(C)(C)C
Ligand InChI: InChI=1S/C21H32F2N2O4/c1-12-20(29-11-21(3,4)5)28-10-18(24-12)19(27)17(25-13(2)26)8-14-6-15(22)9-16(23)7-14/h6-7,9,12,17-20,24,27H,8,10-11H2,1-5H3,(H,25,26)/t12-,17-,18+,19-,20-/m0/s1
Release date: 2017-11-15
Complex of GGTaseIII, farnesyl-Ykt6, and GGPP (PDB entry 6J7X)
Macromolecule: Protein prenyltransferase alpha subunit repeat-containing protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 327 residues
Sequence: MAETSEEVAVLVQRVVKDITNAFRRNPHIDEIGLIPCPEARYNRSPIVLVENKLGVESWCVKFLLPYVHNKLLLYRTRKQWLNRDELIDVTCTLLLLNPDFTTAWNVRKELILSGTLNPIKDLHLGKLALTKFPKSPETWIHRRWVLQQLIQETSLPSFVTKGNLGTIPTERAQRLIQEEMEVCGEAAGRYPSNYNAWSHRIWVLQHLAKLDVKILLDELSSTKHWASMHVSDHSGFHYRQFLLKSLISQTVIDSSVMEQNPLRSEPALVPPKDEEAAVSTEEPRINLPHLLEEEVEFSTDLIDSYPGHETLWCHRRHIFYLQHHLN
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2114
R free: 0.2507
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M NaFormate pH 7, 11% PEG 3350, 30% EG
Matthews coefficient: 4.12
Solvent content (%): 70.12
Ligand: GERANYLGERANYL DIPHOSPHATE (GRG)
Ligand formula: C20 H36 O7 P2
Ligand molecular weight: 450.443
Ligand SMILES: CC(=CCCC(=CCCC(=CCCC(=CCOP(=O)(O)OP(=O)(O)O)C)C)C)C
Ligand InChI: InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)/b18-11+,19-13+,20-15+
Release date: 2020-01-22
Human Xylosyltransferase 1 in complex with peptide QEEEGSGGGQGG (PDB entry 6EJ8)
Macromolecule: Xylosyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.26
Sequence length: 755 residues
Sequence: RALAAPLVHHHHHHALDENLYFQGALADVSRPPHARKTGGSSPETKYDQPPKCDISGKEAISALSRAKSKHCRQEIGETYCRHKLGLLMPEKVTRFCPLEGKANKNVQWDEDSVEYMPANPVRIAFVLVVHGRASRQLQRMFKAIYHKDHFYYIHVDKRSNYLHRQVLQVSRQYSNVRVTPWRMATIWGGASLLSTYLQSMRDLLEMTDWPWDFFINLSAADYPIRTNDQLVAFLSRYRDMNFLKSHGRDNARFIRKQGLDRLFLECDAHMWRLGDRRIPEGIAVDGGSDWFLLNRRFVEYVTFSTDDLVTKMKQFYSYTLLPAESFFHTVLENSPHCDTMVDNNLRITNWNRKLGCKCQYKHIVDWCGCSPNDFKPQDFHRFQQTARPTFFARKFEAVVNQEIIGQLDYYLYGNYPAGTPGLRSYWENVYDEPDGIHSLSDVTLTLYHSFARLGLRRAETSLHTDGENSCRYYPMGHPASVHLYFLADRFQGFLIKHHATNLAVSKLETLETWVMPKKVFKIASPPSDFGRLQFSEVGTDWDAKERLFRNFGGLLGPMDEPVGMQKWGKGPNVTVTVIWVDPVNVIAATYDILIESTAEFTHYKPPLNLPLRPGVWTVKILHHWVPVAETKFLVAPLTFSNRQPIKPEEALKLHNGPLRNAYMEQSFQSLNPVLSLPINPAQVEQARRNAASTGTALEGWLDSLVGGMWTAMDICATGPTACPVMQTCSQTAWSSFSPDPKSELGAVKPDGRLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.1946
R free: 0.2231
Average B factor: 55.3709
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol)
0.1M Bicine/Tris buffer at pH 7.5
0.1M of NPS mix (0.033M of each)
Matthews coefficient: 2.54
Solvent content (%): 51.66
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-05-02
Notum Fragment 863 (PDB entry 7BD6)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1942
R free: 0.2201
Average B factor: 24.079
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.99
Solvent content (%): 38.12
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: 2022-01-12
Crystal structure of the WDR domain of human DCAF1 in complex with OICR-39512 compound (PDB entry 9C1Q)
Macromolecule: DDB1- and CUL4-associated factor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 315 residues
Sequence: GASAFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.15654
R free: 0.19136
Average B factor: 28.3
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG3350, 0.2 M Magnesium formate
Matthews coefficient: 3.21
Solvent content (%): 61.7
Ligand: (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(3-methoxyprop-1-yn-1-yl)-1H-pyrrole-3-carboxamide (A1ATT)
Ligand formula: C24 H19 Cl2 F2 N3 O3
Ligand molecular weight: 506.329
Ligand SMILES: COCC#Cc1c(c(c[nH]1)C(=O)NC(CC(=O)N)c2ccc(c(c2)Cl)F)c3ccc(cc3F)Cl
Ligand InChI: InChI=1S/C24H19Cl2F2N3O3/c1-34-8-2-3-20-23(15-6-5-14(25)10-19(15)28)16(12-30-20)24(33)31-21(11-22(29)32)13-4-7-18(27)17(26)9-13/h4-7,9-10,12,21,30H,8,11H2,1H3,(H2,29,32)(H,31,33)/t21-/m0/s1
Release date: 2024-08-07
Crystal structure of human NEIL1(P2G, E3Q, R242) bound to duplex DNA containing dihydrouracil (DHU) (PDB entry 6LWK)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 295 residues
Sequence: MGQGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGRGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.88
R work: 0.201
R free: 0.2399
Average B factor: 84.067
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000
Matthews coefficient: 2.75
Solvent content (%): 55.23
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: 2021-06-09
Crystal structure of CSF1R kinase domain in complex with DP-6233 (PDB entry 7TNH)
Macromolecule: Macrophage colony-stimulating factor 1 receptor,Fibroblast growth factor receptor 1 chimera
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 338 residues
Sequence: MHHHHHHHHENLYFQGSRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFGKVVEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACTHGGPVLVITEYCCYGDLLNFLRRKRPPGLEYSYNPSHNPEEQLSSRDLLHFSSQVAQGMAFLASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNARLPVKWMAPESIFDCVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMAQPAFAPKNIYSIMQACWALEPTHRPTFQQICSFLQEQAQEDRRERD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.215
R free: 0.269
Average B factor: 71.98
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: CSF1R at 10.7 mg/mL in 50 mM Tris pH 7.5, 200 mM NaCl, 5% glycerol with 5-fold excess of arylamide compound against 10% PEG 10,000, 0.1 M MES pH 6.5 and 0.1 M magnesium acetate soaked over two nights with 1 mM DP-6233 and 20% ethylene glycol as cryo
Matthews coefficient: 2.4
Solvent content (%): 49
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2022-08-24
Human SIRT2 in complex with myristoyl thiourea inhibitor, No.23 (PDB entry 7BOT)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 293 residues
Sequence: GSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2508
R free: 0.3196
Average B factor: 52.484
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.15M Potassium bromide, 30% (w/v) Polyethylene glycol monomethyl ether 2000
Matthews coefficient: 2.03
Solvent content (%): 39.41
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: 2021-03-24
Crystal Structure of the Human vaccinia-related kinase bound to a bis-difluorophenol-aminopyridine inhibitor (PDB entry 6BU6)
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): 1.8
R work: 0.18403
R free: 0.2125
Average B factor: 33.218
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 22% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0
Matthews coefficient: 2.99
Solvent content (%): 58.81
Ligand: 4,4'-(2-aminopyridine-3,5-diyl)bis(2,6-difluorophenol) (E8V)
Ligand formula: C17 H10 F4 N2 O2
Ligand molecular weight: 350.267
Ligand SMILES: c1c(cc(c(c1F)O)F)c2cc(c(nc2)N)c3cc(c(c(c3)F)O)F
Ligand InChI: InChI=1S/C17H10F4N2O2/c18-11-2-7(3-12(19)15(11)24)9-1-10(17(22)23-6-9)8-4-13(20)16(25)14(21)5-8/h1-6,24-25H,(H2,22,23)
Release date: 2017-12-20
proMMP-9desFnII complexed to JNJ0966 INHIBITOR (PDB entry 5UE4)
Macromolecule: Matrix metalloproteinase-9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.35
Sequence length: 236 residues
Sequence: LRTNLTDRQLAEEYLYRYGYTRVAEMRGESKSLGPALLLLQKQLSLPETGELDSATLKAMRTPRCGVPDLGRFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGQGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYGP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1991
R free: 0.2243
Average B factor: 32.84
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 8K 1% glycerol 0.2 M ammonium sulfate 100 mM NaCacodylate
Matthews coefficient: 2.28
Solvent content (%): 45.99
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: 2017-09-13
dAb3/HOIP-RBR-Ligand3 (PDB entry 6SC7)
Macromolecule: E3 ubiquitin-protein ligase RNF31
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.31
Sequence length: 376 residues
Sequence: QECAVCGWALPHNRMQALTSCECTICPDCFRQHFTIALKEKHITDMVCPACGRPDLTDDTQLLSYFSTLDIQLRESLEPDAYALFHKKLTEGVLMRDPKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKRMNDPEYQAQGLAMYLQENGIDCPKCKFSYALARGGCMHFHCTQCRHQFCSGCYNAFYAKNKCPEPNCRVKKSLHGHHPRDCLFYLRDWTALRLQKLLQDNNVMFNTEPPAGARAVPGGGCRVIEQKEVPNGLRDEACGKETPAGYAGLCQAHYKEYLVSLINAHSLDPATLYEVEELETATERYLHVRPQPLAGEDPPAYQARLLQKLTEEVPLGQSIPRRRK
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.56
R work: 0.2239
R free: 0.2674
Average B factor: 66.18
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate, sodium chloride, HEPES
Matthews coefficient: 2.55
Solvent content (%): 51.72
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: 2019-11-27
Crystal structure of apo human proheparanase (PDB entry 5LA4)
Macromolecule: Heparanase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.166
Sequence length: 509 residues
Sequence: GQDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPAYLRFGGTKTDFLIFDPKKESTFEERSYWQSQVNQDICKYGSIPPDVEEKLRLEWPYQEQLLLREHYQKKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.18536
R free: 0.22729
Average B factor: 41.878
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Succinate pH 7.0
17% PEG3350
1:250 dilution seed stock

- Seed stock grown in 0.2M Ammonium Nitrate, 20% PEG3350
Matthews coefficient: 2.32
Solvent content (%): 47
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: 2017-05-31