satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of Human Kallikrein 6 (N217D/I218Y/K224R) in complex with GSK3496783A (PDB entry 6SKB)
Macromolecule: Kallikrein-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 289 residues
Sequence: MPMLSAIVLYVLLAAAAHSAFAAMVHHHHHHSAGLVPRGSGKETAAAKFERQHMDSASGGGDDDDKLVHGGPCDKTSHPYQAALYTSGHLLCGGVLIHPLWVLTAAHCKKPNLQVFLGKHNLGQQESSQEQSSVVRAVIHPDYDAASHDQDIMLLRLARPAKLSELIQPLPLERDCSAQTTSCHILGWGKTADGDFPDTIQCAYIHLVSREECEHAYPGQITQNMLCAGDEKYGKDSCQGDSGGPLVCGDHLRGLVSWGDYPCGSKERPGVYTNVCRYTNWIQKTIQAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.196
R free: 0.229
Average B factor: 35.02
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.6
Crystallization temperature (K): 293
Crystal growth procedure: 100mM Tris-HCl pH 8.6, PEG 4000 18-28%
Matthews coefficient: 1.71
Solvent content (%): 27.95
Ligand: 4-[(3~{S})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]-2-(pyridin-3-ylmethoxy)benzenecarboximidamide (LH5)
Ligand formula: C21 H20 B N3 O3
Ligand molecular weight: 373.213
Ligand SMILES: B1(c2ccccc2CC(O1)c3ccc(c(c3)OCc4cccnc4)C(=N)N)O
Ligand InChI: InChI=1S/C21H20BN3O3/c23-21(24)17-8-7-16(11-20(17)27-13-14-4-3-9-25-12-14)19-10-15-5-1-2-6-18(15)22(26)28-19/h1-9,11-12,19,26H,10,13H2,(H3,23,24)/t19-/m0/s1
Release date: 2019-09-25
Structure of cyclin-dependent kinase 2 with small-molecule ligand 4- fluorobenzoic acid (AT222) in an alternate binding site. (PDB entry 5FP5)
Macromolecule: CYCLIN-DEPENDENT KINASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.16
R work: 0.1866
R free: 0.253
Average B factor: 32.09
Crystallization pH: 7.4
Crystal growth procedure: 10MM HEPES/NAOH PH7.4 15MM NACL PROTEIN CONCENTRATION: 8.6 MG/ML
Matthews coefficient: 2.35
Solvent content (%): 47
Ligand: 4-fluorobenzoic acid (1Y6)
Ligand formula: C7 H5 F O2
Ligand molecular weight: 140.112
Ligand SMILES: c1cc(ccc1C(=O)O)F
Ligand InChI: InChI=1S/C7H5FO2/c8-6-3-1-5(2-4-6)7(9)10/h1-4H,(H,9,10)
Release date: 2015-12-09
CDK2 in complex with a Luciferin derivate (PDB entry 4D1Z)
Macromolecule: CYCLIN-DEPENDENT KINASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.851
R work: 0.1933
R free: 0.2254
Crystal growth procedure: 0 MM HEPES, 20 MM NACL, PH 7.4
Matthews coefficient: 2.1
Solvent content (%): 41.41
Ligand: (4S)-2-(8-hydroxyquinolin-2-yl)-4,5-dihydro-1,3-thiazole-4-carboxylic acid (WG8)
Ligand formula: C13 H10 N2 O3 S
Ligand molecular weight: 274.295
Ligand SMILES: c1cc2ccc(nc2c(c1)O)C3=NC(CS3)C(=O)O
Ligand InChI: InChI=1S/C13H10N2O3S/c16-10-3-1-2-7-4-5-8(14-11(7)10)12-15-9(6-19-12)13(17)18/h1-5,9,16H,6H2,(H,17,18)/t9-/m1/s1
Release date: 2015-03-18
X-ray structure of human PPARalpha ligand binding domain-clofibric acid-SRC1 coactivator peptide co-crystals obtained by delipidation and co-crystallization (PDB entry 7BPY)
Macromolecule: Peroxisome proliferator-activated receptor alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 273 residues
Sequence: GSHMTADLKSLAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYRDMY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.1933
R free: 0.2155
Average B factor: 36.8841
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris (pH 8.5), 30 %(w/v) PEG3350
Matthews coefficient: 2.83
Solvent content (%): 56.51
Ligand: 2-(4-chloranylphenoxy)-2-methyl-propanoic acid (E0O)
Ligand formula: C10 H11 Cl O3
Ligand molecular weight: 214.646
Ligand SMILES: CC(C)(C(=O)O)Oc1ccc(cc1)Cl
Ligand InChI: InChI=1S/C10H11ClO3/c1-10(2,9(12)13)14-8-5-3-7(11)4-6-8/h3-6H,1-2H3,(H,12,13)
Release date: 2020-11-11
Notum-Fragment 201 (PDB entry 7B8U)
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): 1.54
R work: 0.2092
R free: 0.2321
Average B factor: 23.112
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 (%): 38.33
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: 2022-01-12
Cdk2(F80C) with Covalent Adduct TK22 at F80C (PDB entry 6YLK)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 303 residues
Sequence: GPLGSMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVCEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGAKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.216
R free: 0.2648
Average B factor: 39.28
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: Protein solution: 8 mg/mL in 100 mM pH 6.2 phosphate buffer
Reservoir solution: 8-12% PEG3350, 100 mM HEPES pH 7.5-8.15
Matthews coefficient: 1.99
Solvent content (%): 38.09
Ligand: methyl 4-ethyl-1-propanoyl-2,3-dihydroquinoxaline-6-carboxylate (OY2)
Ligand formula: C15 H20 N2 O3
Ligand molecular weight: 276.331
Ligand SMILES: CCC(=O)N1CCN(c2c1ccc(c2)C(=O)OC)CC
Ligand InChI: InChI=1S/C15H20N2O3/c1-4-14(18)17-9-8-16(5-2)13-10-11(15(19)20-3)6-7-12(13)17/h6-7,10H,4-5,8-9H2,1-3H3
Release date: 2020-07-22
CATHEPSIN L IN COMPLEX WITH 4-[cyclopentyl(imidazo[1,2-a]pyridin-2-ylmethyl)amino]-6-morpholino-1,3,5-triazine-2-carbonitrile (PDB entry 5MAJ)
Macromolecule: Cathepsin L1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.15
Sequence length: 220 residues
Sequence: APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1
R work: 0.13639
R free: 0.16999
Average B factor: 17.517
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 25% PEG3350, 0.2M ammonium acetate, 0.1M HEPES
Matthews coefficient: 2.03
Solvent content (%): 39.36
Ligand: ~{N}-cyclopentyl-~{N}-(imidazo[1,2-a]pyridin-2-ylmethyl)-4-(iminomethyl)-6-morpholin-4-yl-1,3,5-triazin-2-amine (7KH)
Ligand formula: C21 H26 N8 O
Ligand molecular weight: 406.484
Ligand SMILES: c1ccn2cc(nc2c1)CN(c3nc(nc(n3)N4CCOCC4)C=N)C5CCCC5
Ligand InChI: InChI=1S/C21H26N8O/c22-13-18-24-20(27-9-11-30-12-10-27)26-21(25-18)29(17-5-1-2-6-17)15-16-14-28-8-4-3-7-19(28)23-16/h3-4,7-8,13-14,17,22H,1-2,5-6,9-12,15H2/b22-13+
Release date: 2017-01-11
Tankyrase 2 catalytic domain in complex with OUL40 (PDB entry 7R3Z)
Macromolecule: Poly [ADP-ribose] polymerase tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 48 residues
Sequence: MAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1967
R free: 0.2449
Average B factor: 43.105
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M Tris pH 8.5, 200 mM lithium sulfate, 20-24% PEG (w/v) PEG 3350
Matthews coefficient: 2.66
Solvent content (%): 53.74
Ligand: 6-methyl-[1,2,4]triazolo[3,4-b][1,3]benzothiazole (I1Q)
Ligand formula: C9 H7 N3 S
Ligand molecular weight: 189.237
Ligand SMILES: Cc1ccc2c(c1)sc3n2cnn3
Ligand InChI: InChI=1S/C9H7N3S/c1-6-2-3-7-8(4-6)13-9-11-10-5-12(7)9/h2-5H,1H3
Release date: 2023-01-25
Importin binding to pol Mu NLS peptide (PDB entry 5W4F)
Macromolecule: Importin subunit alpha-1
Type: Protein, polypeptide(L)
Source organism: Mus musculus
Sequence length: 510 residues
Sequence: MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGSNQGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYFSVEEEEDQNVVPETTSEGFAFQVQDGAPGTFNF
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.984
R work: 0.1695
R free: 0.1988
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES 
0.8 M Sodium Citrate
Matthews coefficient: 2.88
Solvent content (%): 57.26
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2018-06-13
Human Cyclophilin D in complex with N-(5-ethyl-4-oxo-1,2,3,4,5,6-hexahydro-1,5-benzodiazocin-8-yl)-7methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide (PDB entry 7OGI)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MGNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.01
R work: 0.1352
R free: 0.1435
Average B factor: 10.48
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277.15
Crystal growth procedure: 15 % PEG 3350, 0.1M K2HPO4
Matthews coefficient: 2.01
Solvent content (%): 38.88
Ligand: TETRAETHYLENE GLYCOL (PG4)
Ligand formula: C8 H18 O5
Ligand molecular weight: 194.226
Ligand SMILES: C(COCCOCCOCCO)O
Ligand InChI: InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2
Release date: 2022-06-01
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 2g (PDB entry 5NKA)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.377
R work: 0.1599
R free: 0.182
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 37.5% MPD/PEG1000/PEG3350 (MD), 0.25 M Amino Acids Mix (MD), 0.1 M Buffer System 3 (MD) pH8.5
Matthews coefficient: 1.99
Solvent content (%): 38.23
Ligand: 4-[[3-[[5-[(2-chloranyl-6-methyl-phenyl)carbamoyl]-1,3-thiazol-2-yl]amino]phenyl]carbonylamino]cyclohexane-1-carboxylic acid (91H)
Ligand formula: C25 H25 Cl N4 O4 S
Ligand molecular weight: 513.008
Ligand SMILES: Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cccc(c3)C(=O)NC4CCC(CC4)C(=O)O)Cl
Ligand InChI: InChI=1S/C25H25ClN4O4S/c1-14-4-2-7-19(26)21(14)30-23(32)20-13-27-25(35-20)29-18-6-3-5-16(12-18)22(31)28-17-10-8-15(9-11-17)24(33)34/h2-7,12-13,15,17H,8-11H2,1H3,(H,27,29)(H,28,31)(H,30,32)(H,33,34)/t15-,17-
Release date: 2017-06-07
Crystal structure of the catalytic domain of human PARP1 in complex with veliparib (PDB entry 7AAC)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 352 residues
Sequence: GSKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.593
R work: 0.21
R free: 0.242
Average B factor: 24.21
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 2.5 M ammonium sulfate, 0.1 M Tris pH 8.5
Matthews coefficient: 2.28
Solvent content (%): 45.96
Ligand: (2R)-2-(7-carbamoyl-1H-benzimidazol-2-yl)-2-methylpyrrolidinium (78P)
Ligand formula: C13 H16 N4 O
Ligand molecular weight: 244.292
Ligand SMILES: CC1(CCCN1)c2[nH]c3c(cccc3n2)C(=O)N
Ligand InChI: InChI=1S/C13H16N4O/c1-13(6-3-7-15-13)12-16-9-5-2-4-8(11(14)18)10(9)17-12/h2,4-5,15H,3,6-7H2,1H3,(H2,14,18)(H,16,17)/t13-/m1/s1
Release date: 2021-01-13
Discovery of acyl guanidine tryptophan hydroxylase-1 inhibitors (PDB entry 5J6D)
Macromolecule: Tryptophan 5-hydroxylase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.16.4
Sequence length: 307 residues
Sequence: METVPWFPKKISDLDHCANRVLMYGSELDADHPGFKDNVYRKRRKYFADLAMNYKHGDPIPKVEFTEEEIKTWGTVFQELNKLYPTHACREYLKNLPLLSKYCGYREDNIPQLEDVSNFLKERTGFSIRPVAGYLSPRDFLSGLAFRVFHCTQYVRHSSDPFYTPEPDTCHELLGHVPLLAEPSFAQFSQEIGLASLGASEEAVQKLATCYFFTVEFGLCKQDGQLRVFGAGLLSSISELKHALSGHAKVKPFDPKITCKQECLITTFQDVYFVSESFEDAKEKMREFTKTIKRPFGVKYNHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.20984
R free: 0.24812
Average B factor: 46.064
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, CBTP pH 8.4, 2.5 mM TCEP
Matthews coefficient: 2.04
Solvent content (%): 39.76
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2016-05-25
DNA Polymerase Lambda, TTPaS:At Ca2+ Ground State Ternary Complex (PDB entry 7M4K)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 329 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.719
R work: 0.1955
R free: 0.2268
Average B factor: 49.2118
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.85
Solvent content (%): 56.79
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: 2022-07-06
Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 20 mM Mn2+ for 600s (PDB entry 5KFR)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1752
R free: 0.2229
Average B factor: 35.5241
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 17% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.06
Solvent content (%): 40.28
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2016-06-22
Crystal structure of human JMJD2A in complex with compound 44 (PDB entry 5A7S)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.27
Sequence length: 381 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1707
R free: 0.2275
Crystallization pH: 8.5
Crystal growth procedure: 30% PEG3350 -- 0.1M TRIS PH 8.5 -- 0.25M AMMONIUM SULFATE
Matthews coefficient: 2.66
Solvent content (%): 2.66
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: 2016-01-13
Crystal structure of human Pim-1 kinase in complex with an aminooxadiazole-indole inhibitor. (PDB entry 4TY1)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 286 residues
Sequence: MAHHHHHHDEVDGPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.181
R free: 0.2375
Average B factor: 49.747
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 1.0M LiCl, 0.1M TRIS pH8.0, 20% PEG6K
Matthews coefficient: 3.19
Solvent content (%): 61.45
Ligand: N-tert-butyl-5-[3-(4-cyclopropylpyrimidin-2-yl)-1H-indol-5-yl]-1,3,4-oxadiazol-2-amine (38W)
Ligand formula: C21 H22 N6 O
Ligand molecular weight: 374.439
Ligand SMILES: CC(C)(C)Nc1nnc(o1)c2ccc3c(c2)c(c[nH]3)c4nccc(n4)C5CC5
Ligand InChI: InChI=1S/C21H22N6O/c1-21(2,3)25-20-27-26-19(28-20)13-6-7-17-14(10-13)15(11-23-17)18-22-9-8-16(24-18)12-4-5-12/h6-12,23H,4-5H2,1-3H3,(H,25,27)
Release date: 2015-02-04
Carbonic Anhydrase II Inhibitor RA1 (PDB entry 5NXG)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1406
R free: 0.1681
Average B factor: 17.079
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291.15
Crystal growth procedure: 50 mM Tris, 1.6 M Natrium Acetate
Matthews coefficient: 2.05
Solvent content (%): 39.86
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: 2018-01-17
CRYSTAL STRUCTURE OF CSN5(2-257) IN COMPLEX WITH CNS5i-1b (PDB entry 5JOH)
Macromolecule: COP9 signalosome complex subunit 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4
Sequence length: 257 residues
Sequence: GAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISALALLKMVMHARSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTLSSSSLLT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.2263
R free: 0.2482
Average B factor: 71.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: Protein solution: 15 mg/ml CSN5 in 50mM NaCl, 50mM Mes/NaOH pH 6.0, 10uM ZnCl2, 0.5 mM TCEP with 1mM ligand
Crystallization solution: 35% MPD, 0.2M LiSO4, 0.1 M MES/NaOH pH 6.0
Matthews coefficient: 3.09
Solvent content (%): 60.21
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: 2016-11-02
Structure of wild-type human MBD4 bound to a G:T mismatch (PDB entry 5CHZ)
Macromolecule: Methyl-CpG-binding domain protein 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 192 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFMALSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.17369
R free: 0.20899
Average B factor: 26.669
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 21% ethylene glycol
Matthews coefficient: 2.01
Solvent content (%): 36.02
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2016-07-20