satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human Cathepsin-S with bound ligand (PDB entry 5QC9)
Macromolecule: Cathepsin S
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.27
Sequence length: 223 residues
Sequence: ILPDSVDWREKGCVTEVKYQGSCGASWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEILQGGG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.136
R free: 0.169
Average B factor: 16.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Matthews coefficient: 2.25
Solvent content (%): 45.41
Ligand: N-{[5-{1-[3-(dimethylamino)propyl]-5-[(piperidin-4-yl)acetyl]-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridin-3-yl}-2-(trifluoromethyl)phenyl]methyl}-3-methylbut-2-enamide (BG7)
Ligand formula: C31 H43 F3 N6 O2
Ligand molecular weight: 588.707
Ligand SMILES: CC(=CC(=O)NCc1cc(ccc1C(F)(F)F)c2c3c(n(n2)CCCN(C)C)CCN(C3)C(=O)CC4CCNCC4)C
Ligand InChI: InChI=1S/C31H43F3N6O2/c1-21(2)16-28(41)36-19-24-18-23(6-7-26(24)31(32,33)34)30-25-20-39(29(42)17-22-8-11-35-12-9-22)15-10-27(25)40(37-30)14-5-13-38(3)4/h6-7,16,18,22,35H,5,8-15,17,19-20H2,1-4H3,(H,36,41)
Release date: 2017-12-20
Crystal Structure of BMP-2-inducible kinase in complex with an Indazole inhibitor (PDB entry 5IKW)
Macromolecule: BMP-2-inducible protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 310 residues
Sequence: SMSVGVRVFAVGRHQVTLEESLAEGGFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQVSYFAFKFAAADCPVSNINNSSIPSALPEPMTASE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.41
R work: 0.176
R free: 0.216
Average B factor: 53.1
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291.15
Crystal growth procedure: 10% (v/v) Broad MW PEG smear; 3.2 M MgCl2, 100 mM Hepes pH 7.0
Matthews coefficient: 2.75
Solvent content (%): 55.25
Ligand: N-(6-{3-[(cyclopropylsulfonyl)amino]phenyl}-1H-indazol-3-yl)cyclopropanecarboxamide (6BU)
Ligand formula: C20 H20 N4 O3 S
Ligand molecular weight: 396.463
Ligand SMILES: c1cc(cc(c1)NS(=O)(=O)C2CC2)c3ccc4c(c3)[nH]nc4NC(=O)C5CC5
Ligand InChI: InChI=1S/C20H20N4O3S/c25-20(12-4-5-12)21-19-17-9-6-14(11-18(17)22-23-19)13-2-1-3-15(10-13)24-28(26,27)16-7-8-16/h1-3,6,9-12,16,24H,4-5,7-8H2,(H2,21,22,23,25)
Release date: 2016-06-29
Human LOK (STK10) in complex with Bosutinib (PDB entry 5AJQ)
Macromolecule: SERINE/THREONINE-PROTEIN KINASE 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 295 residues
Sequence: SMREYEHVRRDLDPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIETKSEEELEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVLMTLEGDIRLADFGVSAKNLKTLQKRDSFIGTPYWMAPEVVMCETMKDTPYDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDPPTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.21679
R free: 0.25723
Average B factor: 63.681
Crystallization pH: 8.1
Crystal growth procedure: 0.1M TRIS PH 8.1, 0.1M MAGNESIUM CHLORIDE, 30%(W/V) PEG 10000
Matthews coefficient: 2.34
Solvent content (%): 47.5
Ligand: 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile (DB8)
Ligand formula: C26 H29 Cl2 N5 O3
Ligand molecular weight: 530.446
Ligand SMILES: CN1CCN(CC1)CCCOc2cc3c(cc2OC)c(c(cn3)C#N)Nc4cc(c(cc4Cl)Cl)OC
Ligand InChI: InChI=1S/C26H29Cl2N5O3/c1-32-6-8-33(9-7-32)5-4-10-36-25-13-21-18(11-24(25)35-3)26(17(15-29)16-30-21)31-22-14-23(34-2)20(28)12-19(22)27/h11-14,16H,4-10H2,1-3H3,(H,30,31)
Release date: 2015-03-11
Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with an (R)-methyl substitued Fasudil-derivative. (PDB entry 5M71)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Cricetulus griseus
EC number: 2.7.11.11
Sequence length: 353 residues
Sequence: GHMGNAAAAKKGSEQESVKEFLAKAKEEFLKKWESPSQNTAQLDHFDRIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.488
R work: 0.1472
R free: 0.1761
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 277.15
Crystal growth procedure: Drop:
10 mg/ml PKA (0.240 mM)
30 mM MBT (MES/Bis-Tris Puffer pH 6.9)
1 mM DTT
0.1 mM EDTA
75 mM LiCl
0.03 mM Mega 8
0.07mM PKI (Sigma: P7739)
1.2 mM ligand solved in DMSO (50 mM Stock)

Reservoir: 19% Methanol

0.003 mL drop volume, 0.4 mL reservoir volume
Matthews coefficient: 2.15
Solvent content (%): 54.71
Ligand: 5-[[(2~{R})-2-methyl-1,4-diazepan-4-ium-1-yl]sulfonyl]isoquinoline (7K7)
Ligand formula: C15 H20 N3 O2 S
Ligand molecular weight: 306.403
Ligand SMILES: CC1C[NH2+]CCCN1S(=O)(=O)c2cccc3c2ccnc3
Ligand InChI: InChI=1S/C15H19N3O2S/c1-12-10-16-7-3-9-18(12)21(19,20)15-5-2-4-13-11-17-8-6-14(13)15/h2,4-6,8,11-12,16H,3,7,9-10H2,1H3/p+1/t12-/m1/s1
Release date: 2018-06-06
SYK kinase domain in complex with inhibitor GTC000224 (PDB entry 4YJQ)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 281 residues
Sequence: PEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.34
R work: 0.161
R free: 0.1835
Average B factor: 19.19
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 30% Jeffamine ED-2001, 10% Glycerol, 0.1M MES pH6.0, 5mM TCEP
Matthews coefficient: 2.1
Solvent content (%): 41.56
Ligand: 3-[1H-indazol-4-yl(2-{[3-(4-methyl-1,3-oxazol-5-yl)phenyl]amino}pyrimidin-4-yl)amino]propan-1-ol (4DK)
Ligand formula: C24 H23 N7 O2
Ligand molecular weight: 441.485
Ligand SMILES: Cc1c(ocn1)c2cccc(c2)Nc3nccc(n3)N(CCCO)c4cccc5c4cn[nH]5
Ligand InChI: InChI=1S/C24H23N7O2/c1-16-23(33-15-26-16)17-5-2-6-18(13-17)28-24-25-10-9-22(29-24)31(11-4-12-32)21-8-3-7-20-19(21)14-27-30-20/h2-3,5-10,13-15,32H,4,11-12H2,1H3,(H,27,30)(H,25,28,29)
Release date: 2015-09-30
The Crystal Structure of TTBK1 from Biortus. (PDB entry 8XPZ)
Macromolecule: Tau-tubulin kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 332 residues
Sequence: GHMSGGGEQADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKAGTDALLSTSTSTPPQQNTRQTAAMFGVVNV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2009
R free: 0.2733
Average B factor: 58.329
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.5M LiCl, 0.1M Tris-HCl pH8.5, 28% PEG 6000
Matthews coefficient: 2.18
Solvent content (%): 43.63
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: 2024-01-24
Structure of the Hazara virus OTU bound to ubiquitin (PDB entry 7JMS)
Macromolecule: Replicase
Type: Protein, polypeptide(L)
Source organism: Orthonairovirus hazaraense
EC number: 2.7.7.48
Sequence length: 178 residues
Sequence: MDFLEGITWDSVSDIQSVSNPSFTITDYFEVVRQPADGNCFYHSLAELYIPNKSDHAYRLVKNELREAAEKYFPTEPEAAATGMRLDEYLDTALRDNEWGGSLEAAMLSRHLGLTVVIWLVDGSNRVVGATRFGKGSLKTALHLLHSGLTHFDALRLLATEEDPQQETMSGSHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.78
R work: 0.2348
R free: 0.2731
Average B factor: 43.34
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.3 M calcium chloride, 20% PEG 4000
Matthews coefficient: 1.97
Solvent content (%): 37.68
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2020-10-21
Structure of recombinant human beta-glucocerebrosidase in complex with L-carbaxylosyl chloride (PDB entry 8AWR)
Macromolecule: Lysosomal acid glucosylceramidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.45
Sequence length: 497 residues
Sequence: ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWRRQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.1834
R free: 0.2216
Average B factor: 22.777
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Na2SO4, 14% (v/v) PEG3350, 0.25M HEPES, pH 7.0
Matthews coefficient: 2.43
Solvent content (%): 49.44
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: 2024-03-13
Complex between MTH1 and compound 1 (a 7-azaindole-4-ester derivative) (PDB entry 6F20)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 159 residues
Sequence: GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.19727
R free: 0.23518
Average B factor: 30.722
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 3.6
Crystallization temperature (K): 277
Crystal growth procedure: 27% PEG6000, 0.3M Lithium sulfate, 0.1M sodium acetate pH=3.6
Matthews coefficient: 2.32
Solvent content (%): 47.02
Ligand: Ethyl 1H-pyrrolo[2,3-b]pyridine-4-carboxylate (C9E)
Ligand formula: C10 H10 N2 O2
Ligand molecular weight: 190.199
Ligand SMILES: CCOC(=O)c1ccnc2c1cc[nH]2
Ligand InChI: InChI=1S/C10H10N2O2/c1-2-14-10(13)8-4-6-12-9-7(8)3-5-11-9/h3-6H,2H2,1H3,(H,11,12)
Release date: 2018-03-07
STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN INHIBITOR THAT LACKS A ZINC BINDING GROUP (COMPOUND 12) (PDB entry 7LTK)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 376 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.172
R free: 0.198
Average B factor: 32.38
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
Matthews coefficient: 2.44
Solvent content (%): 49.66
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: 2021-05-05
IRAK4 IN COMPLEX WITH inhibitor (PDB entry 6RFI)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 322 residues
Sequence: MHHHHHHHENLYFQGENKSLEVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.31
R work: 0.2096
R free: 0.2365
Average B factor: 59.87
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: pH7.5
Matthews coefficient: 2.48
Solvent content (%): 50.42
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: 2019-10-30
Gcase in complex with small molecule inhibitor 1 (PDB entry 9FAZ)
Macromolecule: Lysosomal acid glucosylceramidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.45
Sequence length: 546 residues
Sequence: MEFSSPSREECPKPLSRVSIMAGSLTGLLLLQAVSWASGARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWRRQHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.15862
R free: 0.19461
Average B factor: 22.307
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M KSCN
25% PEG 3350
Matthews coefficient: 2.16
Solvent content (%): 42.95
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: 2024-07-03
Crystal structure of human microplasmin in complex with kazal-type inhibitor AaTI (PDB entry 7E50)
Macromolecule: AAEL006007-PA
Type: Protein, polypeptide(L)
Source organism: Aedes aegypti
Sequence length: 79 residues
Sequence: SGLEVLFQGPRSDAERGVCACPRIYMPVCGSNLKTYNNDCLLRCEINSDLGRANNLRKIADQACDNLTDNVNDFIPQEY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.218
R free: 0.2748
Average B factor: 49.15
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 0.2 M Ammonium formate, 20 % polyethylene glycol 3350 pH 6.6
Matthews coefficient: 2.15
Solvent content (%): 42.88
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: 2022-02-16
Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors (PDB entry 6X3Y)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 167 residues
Sequence: GHMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1548
R free: 0.1708
Average B factor: 14.12
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG3350, 5% ethanol
Matthews coefficient: 2.74
Solvent content (%): 55.11
Ligand: tert-butyl [(2S)-1-{[(3S,17S)-2,16-dioxo-10,15-dioxa-1,21-diazatricyclo[15.3.1.1~5,9~]docosa-5(22),6,8-trien-3-yl]amino}-3-methyl-1-oxobutan-2-yl]carbamate (UMM)
Ligand formula: C28 H42 N4 O7
Ligand molecular weight: 546.656
Ligand SMILES: CC(C)C(C(=O)NC1Cc2cccc(c2)OCCCCOC(=O)C3CCCN(C1=O)N3)NC(=O)OC(C)(C)C
Ligand InChI: InChI=1S/C28H42N4O7/c1-18(2)23(30-27(36)39-28(3,4)5)24(33)29-22-17-19-10-8-11-20(16-19)37-14-6-7-15-38-26(35)21-12-9-13-32(31-21)25(22)34/h8,10-11,16,18,21-23,31H,6-7,9,12-15,17H2,1-5H3,(H,29,33)(H,30,36)/t21-,22-,23-/m0/s1
Release date: 2020-06-24
CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJ45031882 (PDB entry 6RLQ)
Macromolecule: Protein arginine N-methyltransferase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.320
Sequence length: 644 residues
Sequence: DYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.23
R free: 0.2994
Average B factor: 33.542
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 278
Crystal growth procedure: 30-50% PEG3350, 150mM Ammonium Sulphate
Matthews coefficient: 2.98
Solvent content (%): 58.71
Ligand: (1~{S},2~{R},3~{S},5~{R})-3-[2-(2-azanyl-3-bromanyl-quinolin-7-yl)ethyl]-5-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)cyclop
entane-1,2-diol (K8N)
Ligand formula: C22 H23 Br N6 O2
Ligand molecular weight: 483.361
Ligand SMILES: c1cc2cc(c(nc2cc1CCC3CC(C(C3O)O)n4ccc5c4ncnc5N)N)Br
Ligand InChI: InChI=1S/C22H23BrN6O2/c23-15-8-12-3-1-11(7-16(12)28-21(15)25)2-4-13-9-17(19(31)18(13)30)29-6-5-14-20(24)26-10-27-22(14)29/h1,3,5-8,10,13,17-19,30-31H,2,4,9H2,(H2,25,28)(H2,24,26,27)/t13-,17+,18+,19-/m0/s1
Release date: 2020-07-15
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (H574A) in complex with histone H4 Lys6 tripeptide substrate (PDB entry 5EFN)
Macromolecule: Hdac6 protein
Type: Protein, polypeptide(L)
Source organism: Danio rerio
EC number: 3.5.1.98
Sequence length: 364 residues
Sequence: SNAGGSSPITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPARLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHAAEKDTACGFCFFNTAALTARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAFFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAREFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILEGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAPFWSSLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.804
R work: 0.1622
R free: 0.1941
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris, pH 6.5, 25% PEG3350
Matthews coefficient: 2.44
Solvent content (%): 49.66
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: 2016-07-27
BACE1 in complex with a macrocyclic inhibitor (PDB entry 6NW3)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 390 residues
Sequence: GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.352
R work: 0.1834
R free: 0.2131
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.2 M MgSO4
0.1 M Na citrate
14-20 % PEG4000
Matthews coefficient: 3.08
Solvent content (%): 60.01
Ligand: N-(2-methylpropyl)-N~2~-{[(4S)-17-[(methylsulfonyl)(propyl)amino]-2-oxo-3-azatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15,17-hexaen-4-yl]methyl}-L-norleucinamide (L4J)
Ligand formula: C34 H52 N4 O4 S
Ligand molecular weight: 612.866
Ligand SMILES: CCCCC(C(=O)NCC(C)C)NCC1Cc2cccc(c2)CCCCc3cc(cc(c3)N(CCC)S(=O)(=O)C)C(=O)N1
Ligand InChI: InChI=1S/C34H52N4O4S/c1-6-8-16-32(34(40)36-23-25(3)4)35-24-30-20-27-15-11-14-26(18-27)12-9-10-13-28-19-29(33(39)37-30)22-31(21-28)38(17-7-2)43(5,41)42/h11,14-15,18-19,21-22,25,30,32,35H,6-10,12-13,16-17,20,23-24H2,1-5H3,(H,36,40)(H,37,39)/t30-,32-/m0/s1
Release date: 2019-10-09
Transglutaminase 2 - Open State (PDB entry 9BC2)
Macromolecule: Protein-glutamine gamma-glutamyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.13
Sequence length: 687 residues
Sequence: MAEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYEASVDSLTFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFEDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVVSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAHDQNSNLLIEYFRNEFGEIQGDKSEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTPQEKSEGTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQQDDGSVHKSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRANHLNKLAEKEETGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLNLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLLPLHMGLHKLVVNFESDKLKAVKGFRNVIIGPA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2456
R free: 0.29916
Average B factor: 64.747
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 1.3-1.5M Ammonium Sulfate, 0.050 M Tris.HCl(pH8.9), 0.050M Bicine (pH 9)
Matthews coefficient: 2.54
Solvent content (%): 51.62
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: 2024-07-03