satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of TRIM24 PHD-bromodomain complexed with 2,4-dimethoxy-N-(1-methyl-2-oxo-1,2,3,4-tetrahydroquinolin-6-yl)benzene-1-sulfonamide (3b) (PDB entry 4YAD)
Macromolecule: Transcription intermediary factor 1-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 184 residues
Sequence: SPNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPSHNSEKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.176
R free: 0.208
Average B factor: 28.52
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 2.2-2.4M ammonium sulfate, 0.1M HEPES buffer pH 7.5, 2% PEG400 and 8-9% glycerol
Matthews coefficient: 2.35
Solvent content (%): 47.67
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: 2015-06-24
Crystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P (PDB entry 4ONL)
Macromolecule: Ubiquitin-conjugating enzyme E2 variant 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 153 residues
Sequence: GPLGSPEFMAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQPPEGQTYNN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.1711
R free: 0.1994
Average B factor: 24.14
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM sodium citrate, 15% PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Matthews coefficient: 2.16
Solvent content (%): 43.11
Release date: 2015-05-06
COMPLEMENT FACTOR D IN COMPLEX WITH COMPOUND2 (PDB entry 5FBE)
Macromolecule: Complement factor D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.46
Sequence length: 232 residues
Sequence: ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLASAAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1687
R free: 0.1879
Average B factor: 22.17
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1 MICROLITER PROTEIN SOLUTION WAS MIXED WITH 1 MICROLITER RESERVOIR SOLUTION. PROTEIN SOLUTION: 18 mg/mL FD, 10 mM Tris pH 7.0, 100 mM NaCl; RESERVOIR SOLUTION: 22% PEG3350, 100 mM HEPES pH 7.5; SOAKING AND CRYO: ADDITION of 10 mM COMPOUND2 for 45 min FOLLOWED by the ADDITION OF 0.5 MICROLITER GLYCEROL AND FLASH FREEZING IN LIQUIT NITROGEN.
Matthews coefficient: 2.12
Solvent content (%): 42
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: 2016-10-26
SYK Catalytic Domain Complexed with a Potent Triazine Inhibitor (PDB entry 4RX7)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: MALEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVTDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1806
R free: 0.2034
Average B factor: 30.54
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 0.2M ammonium formate, pH 6.0, vapor diffusion, temperature 293K
Matthews coefficient: 2.26
Solvent content (%): 45.57
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2015-03-18
X-ray structure of furin in complex with the cyclic peptide c[succinyl-Phe-2-Nal-(Arg)4-Lys]-Arg-4-Amba (PDB entry 6HLB)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 482 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1686
R free: 0.1874
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: CRYSTALLIZATION SOLUTION: 100mM MES, 200mM K/NaH2PO4, PH 5.5-6.0, 2 M NaCL, 3% DMSO; RESERVOIR SOLUTION: 3-4M NaCL
Matthews coefficient: 3.77
Solvent content (%): 67.33
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: 2019-02-06
Crystal structure of the C230A mutant of human IBA57 (PDB entry 6GEU)
Macromolecule: Putative transferase CAF17, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1
Sequence length: 314 residues
Sequence: TAGAAWACFRLDGRTLLRVRGPDAAPFLLGLLTNELPLPSPAAAGAPPAARAGYAHFLNVQGRTLYDVILYGLQEHSEVSGFLLECDSSVQGALQKHLALYRIRRKVTVEPHPELRVWAVLPSSPEACGAASLQERAGAAAILIRDPRTARMGWRLLTQDEGPALVPGGRLGDLWDYHQHRYLQGVPEGVRDLPPGVALPLESNLAFMNGVSFTKGAYIGQELTARTHHMGVIRKRLFPVRFLDPLPTSGITPGATVLTASGQTVGKFRAGQGNVGLALLWSEKIKGPLHIRASEGAQVALAASVPDWWPTVSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.15966
R free: 0.20332
Average B factor: 30.846
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES, 20% PEG 3350
Matthews coefficient: 2.58
Solvent content (%): 52.24
Release date: 2019-04-03
Crystal Structure of compound 3 in complex with KRAS G12V C118S GDP and pVHL:ElonginC:ElonginB (PDB entry 8QW6)
Macromolecule: Elongin-B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 104 residues
Sequence: MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.255
R free: 0.2949
Average B factor: 48.29
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 200 mM sodium citrate, 100 mM BIS-TRIS propane pH 8.5, 20% w/v polyethylene glycol 3350
Matthews coefficient: 2.95
Solvent content (%): 58.27
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2023-12-06
Crystal structure of the V122L mutant of human UBR-box domain from UBR2 (PDB entry 5UM3)
Macromolecule: E3 ubiquitin-protein ligase UBR2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 75 residues
Sequence: GPLGSLCGRVFKVGEPTYSCRDCAVDPTCLLCMECFLGSIHRDHRYRMTTSGGGGFCDCGDTEAWKEGPYCQKHE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.198
R work: 0.1369
R free: 0.1583
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M HEPES pH 7.5
25% PEG 4000
Matthews coefficient: 1.72
Solvent content (%): 28.29
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: 2017-03-22
BTK1 SOAKED WITH COMPOUND 25 (PDB entry 7KXP)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 271 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.1735
R free: 0.2149
Average B factor: 22.414
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 3350
0.1 M Bis Tris Propane pH 7.5
0.2 M Sodium acetate trihydrate
Matthews coefficient: 2.45
Solvent content (%): 49.78
Ligand: 3-tert-butyl-N-[(1S)-6-{2-[3-methyl-1-(oxan-4-yl)-1H-pyrazol-4-yl]-1H-imidazo[4,5-b]pyridin-7-yl}-1,2,3,4-tetrahydronaphthalen-1-yl]-1,2,4-oxadiazole-5-carboxamide (X9V)
Ligand formula: C32 H36 N8 O3
Ligand molecular weight: 580.68
Ligand SMILES: Cc1c(cn(n1)C2CCOCC2)c3[nH]c4c(ccnc4n3)c5ccc6c(c5)CCCC6NC(=O)c7nc(no7)C(C)(C)C
Ligand InChI: InChI=1S/C32H36N8O3/c1-18-24(17-40(38-18)21-11-14-42-15-12-21)27-35-26-23(10-13-33-28(26)36-27)20-8-9-22-19(16-20)6-5-7-25(22)34-29(41)30-37-31(39-43-30)32(2,3)4/h8-10,13,16-17,21,25H,5-7,11-12,14-15H2,1-4H3,(H,34,41)(H,33,35,36)/t25-/m0/s1
Release date: 2021-05-19
TEV Cleaved Human ATP Citrate Lyase Bound to 4R-Hydroxycitrate and ADP (PDB entry 5TDM)
Macromolecule: ATP-citrate synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.3.8
Sequence length: 431 residues
Sequence: MSAKAISEQTGKELLYKFICTTSAIQNRFKYARVTPDTDWARLLQDHPWLLSQNLVVKPDQLIKRRGKLGLVGVNLTLDGVKSWLKPRLGQEATVGKATGFLKNFLIEPFVPHSQAEEFYVCIYATREGDYVLFHHEGGVDVGDVDAKAQKLLVGVDEKLNPEDIKKHLLVHAPEDKKEILASFISGLFNFYEDLYFTYLEINPLVVTKDGVYVLDLAAKVDATADYICKVKWGDIEFPPPFGREAYPEEAYIADLDAKSGASLKLTLLNPKGRIWTMVAGGGASVVYSDTICDLGGVNELANYGEYSGAPSEQQTYDYAKTILSLMTREKHPDGKILIIGGSIANFTNVAATFKGIVRAIRDYQGPLKEHEVTIFVRRGGPNYQEGLRVMGEVGKTTGIPIHVFGTETHMTAIVGMALGHRPIPENLYFQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.216
R free: 0.286
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 13% P3350, 100 mM TrisHCl pH 8.7, 125 mM ammonium chloride
Matthews coefficient: 2.73
Solvent content (%): 55.02
Ligand: 3-C-carboxy-2-deoxy-L-threo-pentaric acid (7A2)
Ligand formula: C6 H8 O8
Ligand molecular weight: 208.123
Ligand SMILES: C(C(=O)O)C(C(C(=O)O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C6H8O8/c7-2(8)1-6(14,5(12)13)3(9)4(10)11/h3,9,14H,1H2,(H,7,8)(H,10,11)(H,12,13)/t3-,6-/m0/s1
Release date: 2017-08-09
Carbonic Anhydrase IX like mutant in Complex with Steriod_Sulphamoyl inhibitor AKI_33 (PDB entry 8OKP)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.13159
R free: 0.16515
Average B factor: 15.078
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-H2SO4
Matthews coefficient: 2.07
Solvent content (%): 40.6
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: 2024-04-10
CDC42 binds PAK4 via an extended GTPase-effector interface - 3 peptide: PAK4cat, PAK4-N45, CDC42 (PDB entry 5UPK)
Macromolecule: Serine/threonine-protein kinase PAK 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 48 residues
Sequence: SGSMFGKRKKRVEISAPSNFEHRVHTGFDQHEQKFTGLPRQWQSLIEE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2179
R free: 0.26364
Average B factor: 68.109
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1M HEPES pH 7.5, 22% PEG1,000
Matthews coefficient: 2.34
Solvent content (%): 47.42
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2017-12-27
Peptide EVCKKKK in complex with human cathepsin V C25A mutant (PDB entry 7Q8H)
Macromolecule: Cathepsin L2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.43
Sequence length: 221 residues
Sequence: LPKSVDWRKKGYVTPVKNQKQCGSAWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRPQGNQGCNGGFMARAFQYVKENGGLDSEESYPYVAVDEICKYRPENSVAQDTGFTVVAPGKEKALMKAVATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVVGYGFEGANSQNSKYWLVKNSWGPEWGSNGYVKIAKDKNNHCGIATAASYPNV
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1623
R free: 0.1842
Average B factor: 27.79
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 77% MPD, 23 % of 60 mM TRIS, pH 8
Matthews coefficient: 2.72
Solvent content (%): 54.76
Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL (MPD)
Ligand formula: C6 H14 O2
Ligand molecular weight: 118.174
Ligand SMILES: CC(CC(C)(C)O)O
Ligand InChI: InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
Release date: 2022-11-23
ADP bound TTBK2 kinase domain (PDB entry 6VRF)
Macromolecule: Tau-tubulin kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 299 residues
Sequence: MSGGGEQPDILSVGILVKERWKVLRKIGGGGFGEIYDALDMLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNDRFNYVVMQLQGRNLADLRRSQSRGTFTISTTLRLGRQILESIESIHSVGFLHRDIKPSNFAMGRFPSTCRKCYMLDFGLARQFTNSCGDVRPPRAVAGFRGTVRYASINAHRNREMGRHDDLWSLFYMLVEFVVGQLPWRKIKDKEQVGSIKERYDHRLMLKHLPPEFSIFLDHISSLDYFTKPDYQLLTSVFDNSIKTFGVIESDPFDWEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1742
R free: 0.2092
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 300
Crystal growth procedure: 0.1M TRIS pH 8.5, 10% glycerol and 2.0M Na/K phosphate
Matthews coefficient: 2.81
Solvent content (%): 56.26
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2020-06-03
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_XST00000216b (PDB entry 5QF0)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.707
R work: 0.1871
R free: 0.2121
Average B factor: 38.3865
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.34
Solvent content (%): 63.19
Ligand: 5-phenylthiophene-2-carboxylic acid (JMG)
Ligand formula: C11 H8 O2 S
Ligand molecular weight: 204.245
Ligand SMILES: c1ccc(cc1)c2ccc(s2)C(=O)O
Ligand InChI: InChI=1S/C11H8O2S/c12-11(13)10-7-6-9(14-10)8-4-2-1-3-5-8/h1-7H,(H,12,13)
Release date: 2018-10-10
Structure of human PARP1 catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor (PDB entry 5KPO)
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: HMKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.23753
R free: 0.30275
Average B factor: 41.811
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 2.5M AMMONIUM SULFATE, 100mM TRIS
Matthews coefficient: 2.33
Solvent content (%): 47.3
Ligand: 1-[[3-(4-ethyl-3-oxidanylidene-piperazin-1-yl)carbonyl-4-fluoranyl-phenyl]methyl]quinazoline-2,4-dione (6WY)
Ligand formula: C22 H21 F N4 O4
Ligand molecular weight: 424.425
Ligand SMILES: CCN1CCN(CC1=O)C(=O)c2cc(ccc2F)CN3c4ccccc4C(=O)NC3=O
Ligand InChI: InChI=1S/C22H21FN4O4/c1-2-25-9-10-26(13-19(25)28)21(30)16-11-14(7-8-17(16)23)12-27-18-6-4-3-5-15(18)20(29)24-22(27)31/h3-8,11H,2,9-10,12-13H2,1H3,(H,24,29,31)
Release date: 2016-12-21
Agonist bound human A2a adenosine receptor with D52N mutation at 2.60 A resolution (PDB entry 5WF5)
Macromolecule: Human A2a adenosine receptor T4L chimera
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 504 residues
Sequence: MKTIIALSYIFCLVFADYKDDDDAMGQPVGAPPIMGSSVYITVELAIAVLAILGNVLVCWAVWLNSNLQNVTNYFVVSLAAANIAVGVLAIPFAITISTGFCAACHGCLFIACFVLVLTQSSIFSLLAIAIDRYIAIRIPLRYNGLVTGTRAKGIIAICWVLSFAIGLTPMLGWNNCGQPKEGKNHSQGCGEGQVACLFEDVVPMNYMVYFNFFACVLVPLLLMLGVYLRIFLAARRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYRSTLQKEVHAAKSLAIIVGLFALCWLPLHIINCFTFFCPDCSHAPLWLMYLAIVLSHTNSVVNPFIYAYRIREFRQTFRKIIRSHVLRQQEPFKAHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2138
R free: 0.2509
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 296
Crystal growth procedure: 100 mM sodium citrate pH 5, 24-27% (v/v)
polyethylene glycol (PEG) 400, 30-80 mM MgCl 2 , 5% (v/v) Jeffamine M-600 pH 7 (Hampton)
Matthews coefficient: 2.88
Solvent content (%): 57.22
Ligand: 6-(2,2-diphenylethylamino)-9-[(2R,3R,4S,5S)-5-(ethylcarbamoyl)-3,4-dihydroxy-oxolan-2-yl]-N-[2-[(1-pyridin-2-ylpiperidin-4-yl)carbamoylamino]ethyl]purine-2-carboxamide (UKA)
Ligand formula: C40 H47 N11 O6
Ligand molecular weight: 777.871
Ligand SMILES: CCNC(=O)C1C(C(C(O1)n2cnc3c2nc(nc3NCC(c4ccccc4)c5ccccc5)C(=O)NCCNC(=O)NC6CCN(CC6)c7ccccn7)O)O
Ligand InChI: InChI=1S/C40H47N11O6/c1-2-41-37(54)33-31(52)32(53)39(57-33)51-24-46-30-34(45-23-28(25-11-5-3-6-12-25)26-13-7-4-8-14-26)48-35(49-36(30)51)38(55)43-19-20-44-40(56)47-27-16-21-50(22-17-27)29-15-9-10-18-42-29/h3-15,18,24,27-28,31-33,39,52-53H,2,16-17,19-23H2,1H3,(H,41,54)(H,43,55)(H2,44,47,56)(H,45,48,49)/t31-,32+,33-,39+/m0/s1
Release date: 2018-02-21
MAP2K7 C218S mutant-inhibitor (PDB entry 5Z1E)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 324 residues
Sequence: MTGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTSAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGISGRLVDSKAKTRSAGCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTESPRTSGVLSQPHLPFFRHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.19433
R free: 0.28345
Average B factor: 45.195
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG 3350, sodium citrate
Matthews coefficient: 2.39
Solvent content (%): 48.6
Ligand: N-[3-(6-methyl-1H-indazol-3-yl)phenyl]prop-2-enamide (95U)
Ligand formula: C17 H15 N3 O
Ligand molecular weight: 277.321
Ligand SMILES: Cc1ccc2c(c1)[nH]nc2c3cccc(c3)NC(=O)C=C
Ligand InChI: InChI=1S/C17H15N3O/c1-3-16(21)18-13-6-4-5-12(10-13)17-14-8-7-11(2)9-15(14)19-20-17/h3-10H,1H2,2H3,(H,18,21)(H,19,20)
Release date: 2019-01-02
Crystal structure of human Haspin (GSG2) kinase bound to MU1959 (PDB entry 9FLQ)
Macromolecule: Serine/threonine-protein kinase haspin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 357 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMGECSQKGPVPFSHCLPTEKLQRCEKIGEGVFGEVFQTIADHTPVAIKIIAIEGPDLVNGSHQKTFEEILPEIIISKELSLLSGEVCNRTEGFIGLNSVHCVQGSYPPLLLKAWDHYNSTKGSANDRPDFFKDDQLFIVLEFEFGGIDLEQMRTKLSSLATAKSILHQLTASLAVAEASLRFEHRDLHWGNVLLKKTSLKKLHYTLNGKSSTIPSCGLQVSIIDYTLSRLERDGIVVFCDVSMDEDLFTGDGDYQFDIYRLMKKENNNRWGEYHPYSNVLWLHYLTDKMLKQMTFKTKCNTPAMKQIKRKIQEFHRTMLNFSSATDLLCQHSLFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.17496
R free: 0.20198
Average B factor: 31.859
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 278
Crystal growth procedure: 60% MPD, 0.1M MMT pH 6.0
Matthews coefficient: 2.86
Solvent content (%): 57.01
Ligand: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE)
Ligand formula: C8 H18 N2 O4 S
Ligand molecular weight: 238.305
Ligand SMILES: C1CN(CCN1CCO)CCS(=O)(=O)O
Ligand InChI: InChI=1S/C8H18N2O4S/c11-7-5-9-1-3-10(4-2-9)6-8-15(12,13)14/h11H,1-8H2,(H,12,13,14)
Release date: 2024-09-11