satarupa22/MacromolecularLigandDB huggingface dataset:
FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl [(2R,7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-2-(trifluoromethyl)-2,3,4,5,6,7-hexahydro-1H-8,11-epimino-1,9-benzodiazacyclotridecin-14-yl]carbamate (PDB entry 5QTV)
Macromolecule: Coagulation factor XI
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.174
R free: 0.202
Average B factor: 25.99
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM sodium acetate, pH 4.6, 25% (w/v) MePEG2000, 200 mM ammonium sulfate, then transferred to 100 mM Tris-HCl, pH 7.0, 25% (w/v) MePEG2000, 200 MM ammonium sulfate
Matthews coefficient: 3.45
Solvent content (%): 64.3
Ligand: methyl [(2R,7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-2-(trifluoromethyl)-2,3,4,5,6,7-hexahydro-1H-8,11-epimino-1,9-benzodiazacyclotridecin-14-yl]carbamate (QLS)
Ligand formula: C28 H27 Cl F3 N9 O3
Ligand molecular weight: 630.021
Ligand SMILES: COC(=O)Nc1ccc-2c(c1)NC(CCCCC(c3[nH]c2cn3)NC(=O)C=Cc4cc(ccc4n5cnnn5)Cl)C(F)(F)F
Ligand InChI: InChI=1S/C28H27ClF3N9O3/c1-44-27(43)35-18-8-9-19-21(13-18)36-24(28(30,31)32)5-3-2-4-20(26-33-14-22(19)38-26)37-25(42)11-6-16-12-17(29)7-10-23(16)41-15-34-39-40-41/h6-15,20,24,36H,2-5H2,1H3,(H,33,38)(H,35,43)(H,37,42)/b11-6+/t20-,24+/m0/s1
Release date: 2020-01-29
RNase H complex with streopure ASO and RNA (PDB entry 8SWB)
Macromolecule: Ribonuclease H1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.26.4
Sequence length: 149 residues
Sequence: GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGMDIQWMHVPGHSGFIGNEEADRLAREGAKQSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1836
R free: 0.2238
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4
Crystallization temperature (K): 293
Crystal growth procedure: 1:1 complex : precipitant (0.8 M ammonium sulfate, 0.1 M citrate, pH 4.0), cryoprotection: mother liquor + 1.75 M ammonium sulfate, 1 minute
Matthews coefficient: 2.19
Solvent content (%): 43.85
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: 2024-05-22
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL, beta, gamma dCTP analogue (PDB entry 6CTU)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 16 residues
Sequence: CCGACGTCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1713
R free: 0.2064
Average B factor: 27.1002
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.29
Solvent content (%): 46.34
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: 2018-06-20
Crystal structure of Lysosomal Phospholipase A2 in complex with Isopropyl dodec-11-enylfluorophosphonate (IDFP) (PDB entry 4X91)
Macromolecule: Group XV phospholipase A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1
Sequence length: 380 residues
Sequence: GAGRHPPVVLVPGDLGNQLEAKLDKPTVVHYLCSKKTESYFTIWLNLELLLPVIIDCWIDNIRLVYNKTSRATQFPDGVDVRVPGFGKTFSLEFLDPSKSSVGSYFHTMVESLVGWGYTRGEDVRGAPYDWRRAPNENGPYFLALREMIEEMYQLYGGPVVLVAHSMGNMYTLYFLQRQPQAWKDKYIRAFVSLGAPWGGVAKTLRVLASGDNNRIPVIGPLKIREQQRSAVSTSWLLPYNYTWSPEKVFVQTPTINYTLRDYRKFFQDIGFEDGWLMRQDTEGLVEATMPPGVQLHCLYGTGVPTPDSFYYESFPDRDPKICFGDGDGTVNLKSALQCQAWQSRQEHQVLLQELPGSEHIEMLANATTLAYLKRVLLGP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1833
R free: 0.2136
Average B factor: 35.152
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM HEPES pH 7.5, 3.5% PEG 8000, 28% MPD, 300 mM (NH4)2HPO4
Matthews coefficient: 3.23
Solvent content (%): 61.91
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: 2015-03-11
X-ray structure of the adduct formed upon reaction of oxaliplatin with human angiogenin (PDB entry 7NPM)
Macromolecule: Angiogenin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27
Sequence length: 121 residues
Sequence: DNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1782
R free: 0.2537
Average B factor: 25.6
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.1
Crystallization temperature (K): 298
Crystal growth procedure: 10 % PEG6K, 20 mM sodium citrate pH 5.1, 0.2 M sodium/potassium tartrate
Matthews coefficient: 1.94
Solvent content (%): 36.58
Ligand: PLATINUM (II) ION (PT)
Ligand formula: Pt
Ligand molecular weight: 195.078
Ligand SMILES: [Pt+2]
Ligand InChI: InChI=1S/Pt/q+2
Release date: 2022-03-23
HRV14 3C in complex with single chain antibody GGVV (PDB entry 6KZ0)
Macromolecule: Genome polyprotein
Type: Protein, polypeptide(L)
Source organism: rhinovirus B14
EC number: 3.4.22.29
Sequence length: 184 residues
Sequence: GSGPNTEFALSLLRKNIMTITTSKGEFTGLGIHDRVCVIPTHAQPGDDVLVNGQKIRVKDKYKLVDPENINLELTVLTLDRNEKFRDIRGFISEDLEGVDATLVVHSNNFTNTILEVGPVTMAGLINLSSTPTNRMIRYDYATKTGQCGGVLCATGKIFGIHVGGNGRQGFSAQLKKQYFVEKQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1853
R free: 0.2234
Average B factor: 31.68
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris-HCl, 
25% MPEG5000,
0.2 M Li2SO4
Matthews coefficient: 2.98
Solvent content (%): 58.7
Release date: 2020-05-27
Structure of human ARH3 E41A bound to alpha-NAD+ and magnesium (PDB entry 7ARW)
Macromolecule: ADP-ribose glycohydrolase ARH3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 349 residues
Sequence: GPGSSLSRFRGCLAGALLGDCVGSFYAAHDTVDLTSVLRHVQSLEPDPGTPGSERTEALYYTDDTAMARALVQSLLAKEAFDEVDMAHRFAQEYKKDPDRGYGAGVVTVFKKLLNPKCRDVFEPARAQFNGKGSYGNGGAMRVAGISLAYSSVQDVQKFARLSAQLTHASSLGYNGAILQALAVHLALQGESSSEHFLKQLLGHMEDLEGDAQSVLDARELGMEERPYSSRLKKIGELLDQASVTREEVVSELGNGIAAFESVPTAIYCFLRCMEPDPEIPSAFNSLQRTLIYSISLGGDTDTIATMAGAIAGAYYGMDQVPESWQQSCEGYEETDILAQSLHRVFQKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.31
R work: 0.166
R free: 0.182
Average B factor: 27.42
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 292
Crystal growth procedure: 100 mM ammonium acetate (pH 4.5) and 9% (w/v) PEG10000
Matthews coefficient: 2.34
Solvent content (%): 47.33
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: 2021-06-16
CDK1/CKS1 (PDB entry 4YC6)
Macromolecule: Cyclin-dependent kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 297 residues
Sequence: MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLDNQIKKM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2248
R free: 0.267
Average B factor: 95.396
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.3
Crystallization temperature (K): 277
Crystal growth procedure: 16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4
Matthews coefficient: 2.6
Solvent content (%): 52.5
Release date: 2015-05-20
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with XS039080d (PDB entry 5RAN)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 372 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1828
R free: 0.2248
Average B factor: 41.547
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M bis-tris pH 5.5 21% PEG3350  0.3M magnesium chloride
Matthews coefficient: 2.78
Solvent content (%): 55.81
Ligand: ~{N}-methyl-1-pyridin-4-yl-methanamine (RYP)
Ligand formula: C7 H10 N2
Ligand molecular weight: 122.168
Ligand SMILES: CNCc1ccncc1
Ligand InChI: InChI=1S/C7H10N2/c1-8-6-7-2-4-9-5-3-7/h2-5,8H,6H2,1H3
Release date: 2020-04-22
Notum Inhibitor ARUK3004558 (PDB entry 8BTC)
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: 0.2107
R free: 0.2303
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: 1.93
Solvent content (%): 36.34
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: 2022-12-14
Bruton's tyrosine kinase in complex with N-[(2R)-1-[(3R)-3-(methylcarbamoyl)-1H,2H,3H,4H,9H-pyrido[3,4-b]indol-2-yl]-3-(3-methylphenyl)-1-oxopropan-2-yl]-1H-indazole-5-carboxamide (PDB entry 8U2D)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 270 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1905
R free: 0.2384
Average B factor: 28.43
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 30% EDO_P8K, 0.03M NaF, 0.03M, NaBr, 0.03M NaI, 0.05M Sodium HEPES, 0.05M MOPS pH 7.5
Matthews coefficient: 2.58
Solvent content (%): 52.38
Ligand: (3R)-2-[N-(1H-indazole-5-carbonyl)-3-methyl-D-phenylalanyl]-N-methyl-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxamide (UQX)
Ligand formula: C31 H30 N6 O3
Ligand molecular weight: 534.608
Ligand SMILES: Cc1cccc(c1)CC(C(=O)N2Cc3c(c4ccccc4[nH]3)CC2C(=O)NC)NC(=O)c5ccc6c(c5)cn[nH]6
Ligand InChI: InChI=1S/C31H30N6O3/c1-18-6-5-7-19(12-18)13-26(35-29(38)20-10-11-24-21(14-20)16-33-36-24)31(40)37-17-27-23(15-28(37)30(39)32-2)22-8-3-4-9-25(22)34-27/h3-12,14,16,26,28,34H,13,15,17H2,1-2H3,(H,32,39)(H,33,36)(H,35,38)/t26-,28-/m1/s1
Release date: 2024-01-31
MerTK kinase domain with type 1.5 inhibitor from a DNA-encoded library (PDB entry 7AW2)
Macromolecule: Tyrosine-protein kinase Mer
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 298 residues
Sequence: GSHMEELQNKLEDVVIDRNLLILGRILGEGEFGSVMEGNLKQEDGTSLKVAVKTMKLDNSSQREIEEFLSEAACMKDFSHPNVIRLLGVCIEMSSQGIPKPMVILPFMKYGDLHTYLLYSRLETGPRHIPLQTLLRFMVDIALGMEYLSNRNFLHRDLAARNCMLRDDMTVCVADFGLSKKIYSGDYYRQGRIAKMPVKWIAIESLADRVYTSKSDVWAFGVTMWEIATRGMTPYPGVQNHEMYDYLLHGHRLKQPEDCLDELYEIMYSCWRTDPLDRPTFSVLRLQLERLLESLPDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.207
R free: 0.238
Average B factor: 65.54
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.5 mM protein was crystallised in 4.3 M sodium chloride, 0.1 M Tris pH 8.5 and soaked for 24 h  with 20 mM compound and 20 % DMSO
Matthews coefficient: 2.26
Solvent content (%): 45.56
Ligand: 5-(2'-chloro-[1,1'-biphenyl]-4-yl)-N-(imidazo[1,2-a]pyridin-6-ylmethyl)-N-methyl-1,3,4-oxadiazol-2-amine (S4W)
Ligand formula: C23 H18 Cl N5 O
Ligand molecular weight: 415.875
Ligand SMILES: CN(Cc1ccc2nccn2c1)c3nnc(o3)c4ccc(cc4)c5ccccc5Cl
Ligand InChI: InChI=1S/C23H18ClN5O/c1-28(14-16-6-11-21-25-12-13-29(21)15-16)23-27-26-22(30-23)18-9-7-17(8-10-18)19-4-2-3-5-20(19)24/h2-13,15H,14H2,1H3
Release date: 2021-03-03
Factor Xa complex with GTC000006 (PDB entry 4ZH8)
Macromolecule: Coagulation factor X
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.6
Sequence length: 254 residues
Sequence: IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTRGLPKAKSHAPEVITSSPLK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2065
R free: 0.2553
Average B factor: 27.687
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 16-20% PEG 6K, 50 mM Mes=NaOH pH 5.7-6.0, 5 mM CaCl2 and 50 mM NaCl
Matthews coefficient: 1.9
Solvent content (%): 35.34
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: 2016-01-13
Crystal structure of human heparanase nucleophile mutant (E343Q), in complex with unreacted glucuronic acid configured aziridine probe JJB355 (PDB entry 5L9Z)
Macromolecule: Heparanase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.166
Sequence length: 389 residues
Sequence: DPGKKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGQTSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.16593
R free: 0.19334
Average B factor: 29.93
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 17% PEG3350
0.1 M MES 5.5
0.1 M MgCl2
200 nL:500 nL protein:drop ratio
Matthews coefficient: 2.49
Solvent content (%): 50.64
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2017-05-31
TRK-A IN COMPLEX WITH LIGAND 1a (PDB entry 6PL2)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 311 residues
Sequence: GLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.59
R work: 0.1957
R free: 0.27414
Average B factor: 41.233
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 20mM Tris/HCl
Matthews coefficient: 2.66
Solvent content (%): 53.78
Ligand: N-(3-tert-butyl-1-phenyl-1H-pyrazol-5-yl)-2-{[1-(4-hydroxyphenyl)-1H-tetrazol-5-yl]sulfanyl}acetamide (OOM)
Ligand formula: C22 H23 N7 O2 S
Ligand molecular weight: 449.529
Ligand SMILES: CC(C)(C)c1cc(n(n1)c2ccccc2)NC(=O)CSc3nnnn3c4ccc(cc4)O
Ligand InChI: InChI=1S/C22H23N7O2S/c1-22(2,3)18-13-19(28(25-18)15-7-5-4-6-8-15)23-20(31)14-32-21-24-26-27-29(21)16-9-11-17(30)12-10-16/h4-13,30H,14H2,1-3H3,(H,23,31)
Release date: 2019-09-04
Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dCTP analog (PDB entry 7S9P)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*(FAP)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACXTCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1764
R free: 0.2278
Average B factor: 24.77
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 14-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate
Matthews coefficient: 2.22
Solvent content (%): 44.71
Ligand: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine (XC5)
Ligand formula: C10 H18 N3 O12 P3
Ligand molecular weight: 465.184
Ligand SMILES: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C10H18N3O12P3/c11-8-1-2-13(10(15)12-8)9-3-6(14)7(24-9)4-23-26(16,17)5-27(18,19)25-28(20,21)22/h1-2,6-7,9,14H,3-5H2,(H,16,17)(H,18,19)(H2,11,12,15)(H2,20,21,22)/t6-,7+,9+/m0/s1
Release date: 2022-08-03
Crystal structure of human carbonic anhydrase II in complex with polmacoxib (PDB entry 5GMN)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1547
R free: 0.2018
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris pH 6.5, 28% PEGmme2K
Matthews coefficient: 1.87
Solvent content (%): 34.16
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: 2017-05-24
Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA<sub>2</sub>) Discovered Through X-Ray Fragment Screening (PDB entry 5JAL)
Macromolecule: Platelet-activating factor acetylhydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.47
Sequence length: 388 residues
Sequence: MAAASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTTNQHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.155
R free: 0.196
Average B factor: 29.152
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 297
Crystal growth procedure: 1.0M NaCl, 0.1M HEPES/NaOHpH=7.4, 28.8%w/v PEG 3350
Matthews coefficient: 2.46
Solvent content (%): 49.96
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: 2016-05-25
Human Plasma Kallekrein in complex with 14W (PDB entry 8A3Q)
Macromolecule: Plasma kallikrein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.34
Sequence length: 263 residues
Sequence: NTGDNSVSTTKTSTRIVGGTNSSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILNLSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLNYTEFQKPISLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSDGKAQMQSPA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.801
R work: 0.2353
R free: 0.2725
Average B factor: 49.74
Crystallization method: COUNTER-DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 25% PEG 6K, 0.10 M MES, pH 6.5, 14 mg/mL protein including 20 mM Benzamidine. 1:1 ratio of protein to mother liquor at 1 + 1 microliters over a 500 microliter reservoir at 18 Celsius
Matthews coefficient: 2.13
Solvent content (%): 42.21
Ligand: Unknown ligand (UNL)
Release date: 2022-11-02
Crystal structure of human caspase-1 in complex with Ac-FLTD-CMK (PDB entry 6BZ9)
Macromolecule: Caspase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.36
Sequence length: 178 residues
Sequence: NPAMPTSSGSEGNVKLCSLEEAQRIWKQKSAEIYPIMDKSSRTRLALIICNEEFDSIPRRTGAEVDITGMTMLLQNLGYSVDVKKNLTASDMTTELEAFAHRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQLNAIFNMLNTKNCPSLKDKPKVIIIQACRGDSPGVVWFKD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.796
R work: 0.178
R free: 0.2104
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M sodium formate, 20% w/v PEG3350
Matthews coefficient: 2.66
Solvent content (%): 53.68
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2018-06-13