satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of BACE complex with BMC019 hydrolyzed (PDB entry 5QDC)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 402 residues
Sequence: GPDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.171
R free: 0.195
Average B factor: 51.11
Crystallization method: hanging drop
Crystallization pH: 5
Crystallization temperature (K): 292
Crystal growth procedure: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE PH
5.0. PROTEIN STOCK WAS BACE MUT46B BATCH XIV 7.4MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 6-FOLD EXCESS OF BMC019
ADDED FROM A 50MM STOCK SOLUTION IN DMSO. CRYO-PROTECTANT WAS 1.0M AMMONIUM PHOSPHATE, 0.1M SODIUM CITRATE,
25%(V/V)GLYCEROL, 2.0% DMSO, 1MM BMC019.
Matthews coefficient: 3.05
Solvent content (%): 59.7
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2020-06-03
MLL1 SET N3861I/Q3867L bound to inhibitor 14 (TC-5139) (PDB entry 6U9N)
Macromolecule: Histone-lysine N-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 158 residues
Sequence: SDLPMPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGIVIRSILTDKREKYYDSKGIGCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.227
R free: 0.248
Average B factor: 31.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2.2 M Sodium Malonate pH 7.0
Matthews coefficient: 2.58
Solvent content (%): 52.27
Ligand: 5'-{[(3S)-3-amino-3-carboxypropyl]({1-[(4-chlorophenyl)methyl]azetidin-3-yl}methyl)amino}-5'-deoxyadenosine (Q34)
Ligand formula: C25 H33 Cl N8 O5
Ligand molecular weight: 561.033
Ligand SMILES: c1cc(ccc1CN2CC(C2)CN(CCC(C(=O)O)N)CC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)Cl
Ligand InChI: InChI=1S/C25H33ClN8O5/c26-16-3-1-14(2-4-16)7-33-9-15(10-33)8-32(6-5-17(27)25(37)38)11-18-20(35)21(36)24(39-18)34-13-31-19-22(28)29-12-30-23(19)34/h1-4,12-13,15,17-18,20-21,24,35-36H,5-11,27H2,(H,37,38)(H2,28,29,30)/t17-,18+,20+,21+,24+/m0/s1
Release date: 2020-07-01
Crystal structure of phospholipase A2 with inhibitor (PDB entry 5Y5E)
Macromolecule: Group IIE secretory phospholipase A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.4
Sequence length: 123 residues
Sequence: NLVQFGVMIEKMTGKSALQYGDYGCYCGIGGSHWPVDQTDWCCHAHDCCYGRLEKLGCEPKLEKYLFSVSERGIFCAGRTTCQRLTCECDKRAALCFRRNLGTYNRKYAHYPNKLCTGPTPPC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1926
R free: 0.225
Average B factor: 22.551
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 2.2M Sodium chloride, 0.1M BIS-TRIS propane pH 7.0
Matthews coefficient: 3.44
Solvent content (%): 64.24
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: 2018-06-20
Crystal structure of Fkbp12-IF(SlyD), a chimeric protein of human Fkbp12 and the insert in flap domain of Ecoli SlyD (PDB entry 5I7P)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP1A,FKBP-type peptidyl-prolyl cis-trans isomerase SlyD,Peptidyl-prolyl cis-trans isomerase FKBP1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 161 residues
Sequence: GVQVETISPGDGRTFPKRGQTAVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGQYDENLVQRVPKDVFMGVDELQVGMRFLAETDQGPVPVEITAVEDDHVVVDGNHMLAGQNLVFDVELLKLEAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.002
R work: 0.2189
R free: 0.2483
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20 % PEG3350, 0.1 M MgCl2, 0.1 M Hepes pH 7.5
Matthews coefficient: 3.02
Solvent content (%): 59.23
Release date: 2017-03-08
Structure of human DNA polymerase beta 279NA mutant complexed with G in the template base paired with incoming non-hydrolyzable TTP (PDB entry 4Z6D)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFAKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.1976
R free: 0.2696
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.34
Solvent content (%): 47.39
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: 2016-04-13
Crystal structure of PRMT5:MEP50 with EPZ015666 and SAM (PDB entry 4X61)
Macromolecule: Protein arginine N-methyltransferase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 645 residues
Sequence: MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2055
R free: 0.2603
Average B factor: 65.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.1
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Sodium acetate, 0.1 M Sodium citrate pH 6.1, 10% w/v PEG 4000
Matthews coefficient: 3.01
Solvent content (%): 59.08
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2015-04-22
Human heavy-chain domain antibody in complex with hen egg-white lysozyme (PDB entry 4PGJ)
Macromolecule: Human heavy chain domain antibody
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 121 residues
Sequence: EVQLLESGGGLVQPGGSLRLSCAASGFRFDAEDMGWVRQAPGKGLEWVSSIYGPSGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKYTSPPQNHGFDYWGQGTLVTVSS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.22482
R free: 0.2866
Average B factor: 15.675
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.4
Crystallization temperature (K): 293
Crystal growth procedure: Protein at 4.4 mg/mL in 50 mM Tris (pH 7.5) amd 150 mM NaCl. Well solution contained 28% (w/v) PEG1500, 100 mM Na-citrate (pH 5.4). 400 nL of well solution and protein solution were combined.
Matthews coefficient: 2.61
Solvent content (%): 52.84
Release date: 2015-03-11
Structure of the human JAK1 kinase domain with compound 20 (PDB entry 6N79)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 302 residues
Sequence: GDIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.27
R work: 0.224
R free: 0.27
Average B factor: 41.59
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M MES pH 5-6 and 25-35% PEG 6000
Matthews coefficient: 2.34
Solvent content (%): 47.45
Ligand: N-{5-[5-chloro-2-(difluoromethoxy)phenyl]-1H-pyrazol-4-yl}pyrazolo[1,5-a]pyrimidine-3-carboxamide (KES)
Ligand formula: C17 H11 Cl F2 N6 O2
Ligand molecular weight: 404.758
Ligand SMILES: c1cnc2c(cnn2c1)C(=O)Nc3cn[nH]c3c4cc(ccc4OC(F)F)Cl
Ligand InChI: InChI=1S/C17H11ClF2N6O2/c18-9-2-3-13(28-17(19)20)10(6-9)14-12(8-22-25-14)24-16(27)11-7-23-26-5-1-4-21-15(11)26/h1-8,17H,(H,22,25)(H,24,27)
Release date: 2019-04-24
Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 1 (PDB entry 8OG5)
Macromolecule: DDB1- and CUL4-associated factor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 367 residues
Sequence: GGGREPKQRRQAPINFTSRLNRRASFPKYGGVDGGCFDRHLIFSRFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSALAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVGRQRLAEDEDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1968
R free: 0.2354
Average B factor: 49.263
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES pH6.5, 2.13M Lithium acetate
Matthews coefficient: 2.75
Solvent content (%): 55.21
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: 2023-06-14
HDAC8 Complexed with a Hydroxamic Acid (PDB entry 5FCW)
Macromolecule: Histone deacetylase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 383 residues
Sequence: MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.979
R work: 0.1719
R free: 0.2157
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.3
Crystallization temperature (K): 298
Crystal growth procedure: 4% PEG 3350, 50 mM buffer (MES, pH 5.3)
Matthews coefficient: 2.51
Solvent content (%): 50.98
Ligand: 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide (5YA)
Ligand formula: C17 H13 N O2
Ligand molecular weight: 263.291
Ligand SMILES: c1ccc2c(c1)cccc2c3ccc(cc3)C(=O)NO
Ligand InChI: InChI=1S/C17H13NO2/c19-17(18-20)14-10-8-13(9-11-14)16-7-3-5-12-4-1-2-6-15(12)16/h1-11,20H,(H,18,19)
Release date: 2016-10-26
JAK2 JH2 in complex with XMU-MP-1 (PDB entry 6BRW)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.031
R work: 0.1944
R free: 0.2496
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Tris, pH 8.0
0.2M Sodium acetate
12-20% PEG 4,000
Matthews coefficient: 2.17
Solvent content (%): 43.32
Ligand: 4-[(5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino]benzenesulfonamide (5BS)
Ligand formula: C17 H16 N6 O3 S2
Ligand molecular weight: 416.477
Ligand SMILES: CN1c2ccsc2C(=O)N(c3c1nc(nc3)Nc4ccc(cc4)S(=O)(=O)N)C
Ligand InChI: InChI=1S/C17H16N6O3S2/c1-22-12-7-8-27-14(12)16(24)23(2)13-9-19-17(21-15(13)22)20-10-3-5-11(6-4-10)28(18,25)26/h3-9H,1-2H3,(H2,18,25,26)(H,19,20,21)
Release date: 2018-08-15
Structure of human galactokinase 1 bound with 1-(4-Methoxyphenyl)-3-(4-pyridinyl)urea (PDB entry 6Q90)
Macromolecule: Galactokinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.6
Sequence length: 392 residues
Sequence: HAALRQPQVAELLAEARRAFREEFGAEPELAVSAPGRVNLIGEHTDYNQGLVLPMALELMTVLVGSPRKDGLVSLLTTSEGADEPQRLQFPLPTAQRSLEPGTPRWANYVKGVIQYYPAAPLPGFSAVVVSSVPLGGGLSSSASLEVATYTFLQQLCPDSGTIAARAQVCQQAEHSFAGMPCGIMDQFISLMGQKGHALLIDCRSLETSLVPLSDPKLAVLITNSNVRHSLASSEYPVRRRQCEEVARALGAASLREVQLEELEAARDLVSKEGFRRARHVVGEIRRTAQAAAALRRGDYRAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMTGGGFGGCTVTLLEASAAPHAMRHIQEHYGGTATFYLSQAADGAKVLCL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2201
R free: 0.2766
Average B factor: 43.633
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MOPS/sodium HEPES, pH 7-7.5; 40-50% morpheus precipitant mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1M morpheus carboxylic acids mix (0.02M each of: sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium oxamate, potassium sodium tartrate tetrahydrate
Matthews coefficient: 2.96
Solvent content (%): 58.51
Ligand: 2-(1,3-benzoxazol-2-ylamino)spiro[1,6,7,8-tetrahydroquinazoline-4,1'-cyclohexane]-5-one (HFK)
Ligand formula: C20 H22 N4 O2
Ligand molecular weight: 350.414
Ligand SMILES: c1ccc2c(c1)nc(o2)NC3=NC4(CCCCC4)C5=C(N3)CCCC5=O
Ligand InChI: InChI=1S/C20H22N4O2/c25-15-9-6-8-14-17(15)20(11-4-1-5-12-20)24-18(21-14)23-19-22-13-7-2-3-10-16(13)26-19/h2-3,7,10H,1,4-6,8-9,11-12H2,(H2,21,22,23,24)
Release date: 2019-01-23
Crystal structure of uPA in complex with upain-2-2-W3A (PDB entry 5WXO)
Macromolecule: Urokinase-type plasminogen activator chain B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 253 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKEENGLAL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.18
R free: 0.221
Average B factor: 27.45
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 50mM sodium citrate, pH 4.6, 2.0M ammonium sulfate supplemented with 5% polyethylene glycol 400
Matthews coefficient: 2.07
Solvent content (%): 40.57
Release date: 2018-07-11
High-resolution crystal structure of human JAK2 kinase domain (JH1) bound to type-II inhibitor BBT594 (PDB entry 7RN6)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 298 residues
Sequence: GAFARDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1892
R free: 0.2136
Average B factor: 24.4269
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 1.8M Sodium Malonate pH 6.5
Matthews coefficient: 2.68
Solvent content (%): 54.08
Ligand: 5-{[6-(acetylamino)pyrimidin-4-yl]oxy}-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}-2,3-dihydro-1H-indole-1-carboxamide (046)
Ligand formula: C28 H30 F3 N7 O3
Ligand molecular weight: 569.578
Ligand SMILES: CC(=O)Nc1cc(ncn1)Oc2ccc3c(c2)CCN3C(=O)Nc4ccc(c(c4)C(F)(F)F)CN5CCN(CC5)C
Ligand InChI: InChI=1S/C28H30F3N7O3/c1-18(39)34-25-15-26(33-17-32-25)41-22-5-6-24-19(13-22)7-8-38(24)27(40)35-21-4-3-20(23(14-21)28(29,30)31)16-37-11-9-36(2)10-12-37/h3-6,13-15,17H,7-12,16H2,1-2H3,(H,35,40)(H,32,33,34,39)
Release date: 2021-11-03
Crystal structure of chimeric carbonic anhydrase VA with 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide (PDB entry 7NZT)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNTGYLFQVEFDDSQDKAVLKGGPLDGTYRLKQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDYGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLTECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.1225
R free: 0.1657
Average B factor: 14.846
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate
Matthews coefficient: 2.07
Solvent content (%): 40.45
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: 2022-04-13
Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dA (PDB entry 5DBB)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.2056
R free: 0.2645
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.39
Solvent content (%): 48.62
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2015-11-11
Crystal structure of the CK2a1-go289 complex (PDB entry 6A1C)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 340 residues
Sequence: GPLGSMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.68
R work: 0.13751
R free: 0.19627
Average B factor: 23.406
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: ethyleneglycol
Matthews coefficient: 2
Solvent content (%): 38.41
Ligand: 5-bromanyl-2-methoxy-4-[(E)-(3-methylsulfanyl-5-phenyl-1,2,4-triazol-4-yl)iminomethyl]phenol (9NX)
Ligand formula: C17 H15 Br N4 O2 S
Ligand molecular weight: 419.296
Ligand SMILES: COc1cc(c(cc1O)Br)C=Nn2c(nnc2SC)c3ccccc3
Ligand InChI: InChI=1S/C17H15BrN4O2S/c1-24-15-8-12(13(18)9-14(15)23)10-19-22-16(20-21-17(22)25-2)11-6-4-3-5-7-11/h3-10,23H,1-2H3/b19-10+
Release date: 2019-03-06
Carbonic anhydrase inhibitors: Design and synthesis of new heteroaryl-N-carbonylbenzenesulfonamides targeting druggable human carbonic anhydrase isoforms (hCA VII, hCA IX, and hCA XIV) (PDB entry 4Z1J)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 258 residues
Sequence: HHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.27
R work: 0.137
R free: 0.1703
Average B factor: 12.726
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 50mM Tris-HCl, 1,6 M Sodium Citrate
Matthews coefficient: 2.09
Solvent content (%): 41.13
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: 2015-08-26
Human angiogenin ALS variant T80S (PDB entry 5M9P)
Macromolecule: Angiogenin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27
Sequence length: 124 residues
Sequence: MQDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTSCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFRRP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.23846
R free: 0.28522
Average B factor: 21.71
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.2 M ammonium sulphate
0.1 M bis-tris propane
25% PEG 3350
Matthews coefficient: 2.3
Solvent content (%): 46.58
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: 2017-02-22