satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of Aurora-A kinase in complex with N-Myc (PDB entry 5G1X)
Macromolecule: AURORA KINASE A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 285 residues
Sequence: GAMESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPSNAQNKESASKQS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.1762
R free: 0.1951
Average B factor: 28.09
Crystallization pH: 9
Crystal growth procedure: 100 MM BICINE PH 9.0, 20% PEG 6000
Matthews coefficient: 2.49
Solvent content (%): 50.6
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: 2016-11-16
TDG enzyme-substrate complex (PDB entry 5HF7)
Macromolecule: G/T mismatch-specific thymine DNA glycosylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2.29
Sequence length: 227 residues
Sequence: SKKSGKSAKSKEKQEKITDTFKVKRKVDRFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNMDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.54
R work: 0.1858
R free: 0.2143
Average B factor: 44.43
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 0.2 M Ammonium chloride, 20% PEG 3350
Matthews coefficient: 2.41
Solvent content (%): 49
Release date: 2016-09-28
Crystal structure of BACE complex with BMC017 (PDB entry 5QD2)
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): 2.5
R work: 0.157
R free: 0.205
Average B factor: 46.42
Crystallization method: hanging drop
Crystallization temperature (K): 292
Crystal growth procedure: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM SULFATE. PROTEIN STOCK WAS BACE
MUT46B BATCH XII 8.45MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 5-FOLD EXCESS OF BMC017 ADDED FROM A 50MM STOCK
SOLUTION IN DMSO (2.0% DMSO IN DROP). CRYO- PROTECTANT WAS 1.2M AMMONIUM SULFATE, 25%(V/V)GLYCEROL, 2.0% DMSO, 1MM
BMC017.
Matthews coefficient: 3.07
Solvent content (%): 59.88
Ligand: (4S)-4-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-19-(methoxymethyl)-11,16-dioxa-3-azatricyclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaen-2-one (E6J)
Ligand formula: C33 H42 N2 O5
Ligand molecular weight: 546.697
Ligand SMILES: CC(C)c1cccc(c1)CNCC(C2Cc3cccc(c3)OCCCCOc4cc(cc(c4)C(=O)N2)COC)O
Ligand InChI: InChI=1S/C33H42N2O5/c1-23(2)27-10-6-9-25(14-27)20-34-21-32(36)31-18-24-8-7-11-29(16-24)39-12-4-5-13-40-30-17-26(22-38-3)15-28(19-30)33(37)35-31/h6-11,14-17,19,23,31-32,34,36H,4-5,12-13,18,20-22H2,1-3H3,(H,35,37)/t31-,32+/m0/s1
Release date: 2020-06-03
CLK3 bound with beta-carboline KH-CARB13 (Cpd 3) (PDB entry 6YU1)
Macromolecule: Dual specificity protein kinase CLK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 360 residues
Sequence: SMQSSKRSSRSVEDDKEGHLVCRIGDWLQERYEIVGNLGEGTFGKVVECLDHARGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVATRHYRPPEVILELGWAQPCDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSFHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1756
R free: 0.2029
Average B factor: 27.445
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 18% PEG 3350, 0,2M Na/K PO4, 10% Ethylene Glycol
Matthews coefficient: 2.97
Solvent content (%): 58.56
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: 2020-07-15
X-ray structure of furin in complex with the canavanine derived inhibitor 4-guanidinomethyl-phenylacetyl-Canavanine-Tle-Arg-Amba (PDB entry 6YD3)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 480 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1595
R free: 0.1854
Average B factor: 32.04
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; RESERVOIR SOLUTION: 3-4M NACL
Matthews coefficient: 3.72
Solvent content (%): 66.96
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: 2021-02-17
Corticotropin-releasing hormone receptor 1(CRF1R) bound with BMK-C203 by XFEL (PDB entry 8GTM)
Macromolecule: Isoform CRF-R2 of Corticotropin-releasing factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 284 residues
Sequence: MEILNEEKKSKVHYHVAAIINYLGHCISLVALLVAFVLFLRARSIRCLRNIIHANLIAAFILRNATWFVVQLTMSPEVHQSNVGWCRLVTAAYNYFHVTNFFWMFGEGCYLHTAIVLTYSTDRLRAWMFICIGWGVPFPIIVAWAIGKLYYDNEKCWAGKRPGVYTDYIYQGPMALVLLINFIFLFNIVRILMTKLRASTTSETIQARKAVKATLVLLPLLGITYMLAFVNPGEDEVSRVVFIYFNAFLESFQGFFVSVFACFLNSEVRSAAAAHHHHHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2193
R free: 0.2602
Average B factor: 66.47
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.05M Na-Citrate(4.5), 0.06M NaCl
20~30% PEG 400(w/v)
Matthews coefficient: 2.82
Solvent content (%): 56.42
Ligand: 7-(4-bromanyl-2,6-dimethoxy-phenyl)-4,8-dimethyl-~{N},~{N}-bis[4,4,4-tris(fluoranyl)butyl]-1$l^{4},3,5,9-tetrazabicyclo[4.3.0]nona-1(6),2,4,8-tetraen-2-amine (0VI)
Ligand formula: C23 H27 Br F6 N5 O2
Ligand molecular weight: 599.387
Ligand SMILES: CC1=N[N]2=C(C1c3c(cc(cc3OC)Br)OC)N=C(N=C2N(CCCC(F)(F)F)CCCC(F)(F)F)C
Ligand InChI: InChI=1S/C23H27BrF6N5O2/c1-13-18(19-16(36-3)11-15(24)12-17(19)37-4)20-31-14(2)32-21(35(20)33-13)34(9-5-7-22(25,26)27)10-6-8-23(28,29)30/h11-12,18H,5-10H2,1-4H3/t18-/m0/s1
Release date: 2023-09-13
Structure of CHK1 10-pt. mutant complex with AMP-PNP (PDB entry 5OOP)
Macromolecule: Serine/threonine-protein kinase Chk1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICILKMLNHENVIKFYGHRREGNIQYLFMELASGGSLFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPHNLLLDERDNLKIADYSLATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRPRVTSGGVSESPSGHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1565
R free: 0.1971
Average B factor: 34.655
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7% PEG 8000, 0.1 M MES buffer, pH 6.5, 20% ethylene glycol
Matthews coefficient: 2.33
Solvent content (%): 47.29
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: 2017-10-25
APE1 Mn-bound phosphorothioate substrate complex with abasic ribonucleotide DNA (PDB entry 7LPJ)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 276 residues
Sequence: ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.56
R work: 0.1829
R free: 0.2481
Average B factor: 39.69
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM tri-Sodium Citrate (pH 4), 100 mM NaCl, 10% Peg 6,000
Matthews coefficient: 2.52
Solvent content (%): 51.26
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: 2021-08-04
Crystals Structure of B-Raf kinase domain in complex with an Imidazopyridinyl benzamide inhibitor (PDB entry 6B8U)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 281 residues
Sequence: GSDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.1784
R free: 0.2184
Average B factor: 41.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.7
Crystallization temperature (K): 277
Crystal growth procedure: 10% PEG8000, 0.1 M sodium citrate pH 4.7, and 0.2 M sodium chloride
Matthews coefficient: 2.82
Solvent content (%): 56.38
Ligand: ~{N}-[3-(2-acetamidoimidazo[1,2-a]pyridin-6-yl)-4-methyl-phenyl]-3-(trifluoromethyl)benzamide (8EN)
Ligand formula: C24 H19 F3 N4 O2
Ligand molecular weight: 452.428
Ligand SMILES: Cc1ccc(cc1c2ccc3nc(cn3c2)NC(=O)C)NC(=O)c4cccc(c4)C(F)(F)F
Ligand InChI: InChI=1S/C24H19F3N4O2/c1-14-6-8-19(29-23(33)16-4-3-5-18(10-16)24(25,26)27)11-20(14)17-7-9-22-30-21(28-15(2)32)13-31(22)12-17/h3-13H,1-2H3,(H,28,32)(H,29,33)
Release date: 2017-11-22
Crystal structure of CREBBP bromodomain complexed with CBP007 (PDB entry 5MPZ)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1577
R free: 0.1763
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M MgCl2, 0.1 M Bis-Tris, pH 6.5, 5% v/v ethylene glycol, 23% PEG3350
Matthews coefficient: 2.08
Solvent content (%): 40.93
Ligand: methyl 2-oxidanylidene-3~{H}-1,3-benzoxazole-6-carboxylate (4I8)
Ligand formula: C9 H7 N O4
Ligand molecular weight: 193.156
Ligand SMILES: COC(=O)c1ccc2c(c1)OC(=O)N2
Ligand InChI: InChI=1S/C9H7NO4/c1-13-8(11)5-2-3-6-7(4-5)14-9(12)10-6/h2-4H,1H3,(H,10,12)
Release date: 2017-05-10
Crystal Structure of mGluR5 in complex with MMPEP at 2.2 A (PDB entry 6FFI)
Macromolecule: Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 444 residues
Sequence: AASPVQYLRWGDPAPIAAVVFACLGLLATLFVTVVFIIYRDTPVVKSSSRELCYIILAGICLGYLCTFCLIAKPKQIYCYLQRIGIGLSPAMSYSALVTKTYRAARILAMSKKNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKICTKKPRFMSACAQLVIAFILICIQLGIIVALFIMEPPDIMHDYPSIREVYLICNTTNLGVVAPLGYNGLLILACTFYAFKTRNVPANFNEAKYIAFTMYTTCIIWLAFVPIYFGSNYKIITMCFSVSLSATVALGCMFVPKVYIILAKPERNVRSAAAAHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2264
R free: 0.2693
Average B factor: 28.89
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 6.8
Crystallization temperature (K): 293.1
Crystal growth procedure: 24-34% V/V PEG400, 0.2 M AMMONIUM PHOSPHATE DIBASIC, 0.1 M MES, PH 6.8
Matthews coefficient: 2.52
Solvent content (%): 51.16
Ligand: OLEIC ACID (OLA)
Ligand formula: C18 H34 O2
Ligand molecular weight: 282.461
Ligand SMILES: CCCCCCCCC=CCCCCCCCC(=O)O
Ligand InChI: InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9-
Release date: 2018-03-07
The crystal structure of the GST-like domains complex of EPRS-AIMP2 mutant S156D (PDB entry 5A1N)
Macromolecule: BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.15
Sequence length: 175 residues
Sequence: MATLSLTVNSGDPPLGALLAVEHVKDDVSISVEEGKENILHVSENVIFTDVNSILRYLARVATTAGLYGSNLMEHTEIDHWLEFSATKLSSSDSFTSTINELNHSLSLRTYLVGNSLSLADLSVWATLKGNAAWQEQLKQKKAPVHVKRWFGFLEAQQAFQSVGTKWDVSTTKAR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1933
R free: 0.2313
Crystallization pH: 5.5
Crystal growth procedure: 17% PEG 3350, 0.1M BIS-TRIS PH 5.5, 2MM DTT
Matthews coefficient: 2.73
Solvent content (%): 55.01
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: 2016-06-01
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA000470b (PDB entry 7FQU)
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): 1.86
R work: 0.1828
R free: 0.2229
Average B factor: 40.401
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Matthews coefficient: 3.29
Solvent content (%): 62.65
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2022-11-23
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOOA000497a (PDB entry 5QFW)
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): 1.662
R work: 0.1934
R free: 0.2209
Average B factor: 40.4113
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: 3.32
Solvent content (%): 62.92
Ligand: (1S,4R,5S,6R)-2-(methylsulfonyl)-2-azabicyclo[3.3.1]nonane-4,6-diol (JKA)
Ligand formula: C9 H17 N O4 S
Ligand molecular weight: 235.301
Ligand SMILES: CS(=O)(=O)N1CC(C2CC1CCC2O)O
Ligand InChI: InChI=1S/C9H17NO4S/c1-15(13,14)10-5-9(12)7-4-6(10)2-3-8(7)11/h6-9,11-12H,2-5H2,1H3/t6-,7-,8+,9-/m0/s1
Release date: 2018-10-10
Carbonic Anhydrase CAIX mimic in complex with inhibitor FBSA (PDB entry 6RZX)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVVKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1
R work: 0.1279
R free: 0.1504
Average B factor: 15.319
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 (%): 40.52
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: 2020-06-03
Crystal Structure of human cyclic GMP-AMP synthase in complex with 6-(2-chloro-4-methylphenyl)-3-(2-phenylethyl)benzimidazole-4-carboxylic acid (PDB entry 7FUK)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.606
R work: 0.1907
R free: 0.236
Average B factor: 36.9652
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals.
Matthews coefficient: 2.13
Solvent content (%): 42.23
Ligand: (5M)-5-(2-chloro-4-methylphenyl)-1-(2-phenylethyl)-1H-benzimidazole-7-carboxylic acid (YQU)
Ligand formula: C23 H19 Cl N2 O2
Ligand molecular weight: 390.862
Ligand SMILES: Cc1ccc(c(c1)Cl)c2cc(c3c(c2)ncn3CCc4ccccc4)C(=O)O
Ligand InChI: InChI=1S/C23H19ClN2O2/c1-15-7-8-18(20(24)11-15)17-12-19(23(27)28)22-21(13-17)25-14-26(22)10-9-16-5-3-2-4-6-16/h2-8,11-14H,9-10H2,1H3,(H,27,28)
Release date: 2024-02-21
PDE2 catalytic domain complexed with inhibitors (PDB entry 5U7L)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 345 residues
Sequence: GSAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.2085
R free: 0.2813
Average B factor: 32.379
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 25% PEG 3350, 0.1 M Tris, pH 8.5, and 0.2 M MgCl2
Matthews coefficient: 2.23
Solvent content (%): 44.96
Ligand: (3R)-1-{3-[5-(4-ethylphenyl)-1-methyl-1H-pyrazol-4-yl]-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-yl}-N,N-dimethylpyrrolidin-3-amine (7Y4)
Ligand formula: C24 H30 N8
Ligand molecular weight: 430.549
Ligand SMILES: CCc1ccc(cc1)c2c(cnn2C)c3c4c(ncnc4N5CCC(C5)N(C)C)n(n3)C
Ligand InChI: InChI=1S/C24H30N8/c1-6-16-7-9-17(10-8-16)22-19(13-27-30(22)4)21-20-23(31(5)28-21)25-15-26-24(20)32-12-11-18(14-32)29(2)3/h7-10,13,15,18H,6,11-12,14H2,1-5H3/t18-/m1/s1
Release date: 2017-06-28
The X-ray structure of human M189I PGK-1 mutant in partially closed conformation (PDB entry 5M6Z)
Macromolecule: Phosphoglycerate kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.2.3
Sequence length: 416 residues
Sequence: SLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLIKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.18281
R free: 0.22295
Average B factor: 27.804
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.6
Crystallization temperature (K): 294
Crystal growth procedure: 2.5 M Na//KPO4, pH=8.6
Matthews coefficient: 2.02
Solvent content (%): 38.51
Ligand: 3-PHOSPHOGLYCERIC ACID (3PG)
Ligand formula: C3 H7 O7 P
Ligand molecular weight: 186.057
Ligand SMILES: C(C(C(=O)O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C3H7O7P/c4-2(3(5)6)1-10-11(7,8)9/h2,4H,1H2,(H,5,6)(H2,7,8,9)/t2-/m1/s1
Release date: 2017-11-29