satarupa22/MacromolecularLigandDB huggingface dataset:
STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A BENZOTRIAZOLE FRAGMENT (PDB entry 6R8Q)
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): 1.5
R work: 0.1546
R free: 0.1946
Average B factor: 21.8566
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 295
Crystal growth procedure: 1.4 M AMMONIUM SULPHATE, 
0.1 M CITRIC ACID, 
PH 4.0
Matthews coefficient: 1.92
Solvent content (%): 36.04
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: 2019-05-08
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z1745658474 (PDB entry 5RYL)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1726
R free: 0.2014
Average B factor: 20.924
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.07
Solvent content (%): 40.65
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: 2020-11-11
Crystal structure of the TMPRSS2 zymogen in complex with the nanobody A07 (PDB entry 8S0L)
Macromolecule: Transmembrane protease serine 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.122
Sequence length: 395 residues
Sequence: KFMGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSWHPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHSDACSSKAVVSLRCIACGVNLNSSRQSRIVGGESALPGAWPWQVSLHVQNVHVCGGSIITPEWIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVDSCQGDAGGPLVTSKNNIWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRADGGPFEDDDDK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1769
R free: 0.2154
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 20 %w/v PEG 3350, 0.05 M HEPES (pH 7.0), 1 %w/v Tryptone, 0.001 %w/v NaN3
Matthews coefficient: 2.65
Solvent content (%): 53.54
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: 2024-06-26
Crystal structure of human tankyrase 2 in complex with TA-21 (PDB entry 4UHG)
Macromolecule: TANKYRASE-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 240 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.17514
R free: 0.20362
Average B factor: 20.837
Crystallization pH: 8.5
Crystal growth procedure: 0.2 M LISO4, 0.1 M TRIS HCL, 22% PEG3350, PH 8.5
Matthews coefficient: 2.5
Solvent content (%): 50
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: 2016-04-13
Monobody 12VC3 Bound to HRAS(WT) (PDB entry 7L0F)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 167 residues
Sequence: SMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1594
R free: 0.1912
Average B factor: 35.681
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.225 M Potassium sodium tartrate tetrahydrate, 15% w/v Polyethylene glycol 3,350
Matthews coefficient: 2.52
Solvent content (%): 51.1
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: 2021-03-24
Crystal structure of ASK1 kinase domain with a potent inhibitor (analog 6) (PDB entry 5VIL)
Macromolecule: Mitogen-activated protein kinase kinase kinase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 293 residues
Sequence: RSTEEGDCESDLLEYDYEYDENGDRVVLGKGTYGIVYAGRDLSNQVRIAIKEIPERDSRYSQPLHEEIALHKHLKHKNIVQYLGSFSENGFIKIFMEQVPGGSLSALLRSKWGPLKDNEQTIGFYTKQILEGLKYLHDNQIVHRDIKGDNVLINTYSGVLKISDFGTSKRLAGINPCTETFTGTLQYMAPEIIDKGPRGYGKAADIWSLGCTIIEMATGKPPFYELGEPQAAMFKVGMFKVHPEIPESMSAEAKAFILKCFEPDPDKRACANDLLVDEFLKVSSKKKKTQPKL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.64
R work: 0.18
R free: 0.213
Average B factor: 122.72
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 0.2M ammonium chloride, 0.1M Bis-Tris (pH 6.1-6.6), and 10% glycerol.
Matthews coefficient: 2.74
Solvent content (%): 55.13
Ligand: 2-methoxy-N-{6-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]pyridin-2-yl}-5-sulfamoylbenzamide (9E1)
Ligand formula: C18 H20 N6 O4 S
Ligand molecular weight: 416.454
Ligand SMILES: CC(C)n1cnnc1c2cccc(n2)NC(=O)c3cc(ccc3OC)S(=O)(=O)N
Ligand InChI: InChI=1S/C18H20N6O4S/c1-11(2)24-10-20-23-17(24)14-5-4-6-16(21-14)22-18(25)13-9-12(29(19,26)27)7-8-15(13)28-3/h4-11H,1-3H3,(H2,19,26,27)(H,21,22,25)
Release date: 2018-01-17
TrkA JM-kinase with 1-(9{H}-fluoren-9-yl)-3-(2-methyl-4-phenyl-pyrimidin-5-yl)urea (PDB entry 5KMI)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 329 residues
Sequence: SSLSPTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.208
R free: 0.2466
Average B factor: 38.19
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside
Matthews coefficient: 2.39
Solvent content (%): 48.43
Ligand: 1-(9~{H}-fluoren-9-yl)-3-(2-methyl-4-phenyl-pyrimidin-5-yl)urea (6UE)
Ligand formula: C25 H20 N4 O
Ligand molecular weight: 392.453
Ligand SMILES: Cc1ncc(c(n1)c2ccccc2)NC(=O)NC3c4ccccc4-c5c3cccc5
Ligand InChI: InChI=1S/C25H20N4O/c1-16-26-15-22(23(27-16)17-9-3-2-4-10-17)28-25(30)29-24-20-13-7-5-11-18(20)19-12-6-8-14-21(19)24/h2-15,24H,1H3,(H2,28,29,30)
Release date: 2016-12-28
KRAS 1-169 G12C Mutant at 240k (PDB entry 8TXK)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 169 residues
Sequence: MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.38
R work: 0.1949
R free: 0.2206
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 200mM Na Acetate pH 3.6
100mM Tris pH 8.5
20% PEG 3350
1mM DTT
Matthews coefficient: 2.01
Solvent content (%): 38.92
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: 2024-08-28
Binary Complex of Human DNA Polymerase Mu with MndTTP (PDB entry 6IPJ)
Macromolecule: DNA-directed DNA/RNA polymerase mu,DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.19767
R free: 0.23955
Average B factor: 27.72
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M HEPES pH 7.5, 1.5 M Li2SO4
Matthews coefficient: 2.45
Solvent content (%): 49.75
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: 2019-05-29
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434865 (PDB entry 5RWE)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.34
R work: 0.1702
R free: 0.1949
Average B factor: 17.175
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.09
Solvent content (%): 41.2
Ligand: 4-[2-(phenylsulfanyl)ethyl]morpholine (JJG)
Ligand formula: C12 H17 N O S
Ligand molecular weight: 223.334
Ligand SMILES: c1ccc(cc1)SCCN2CCOCC2
Ligand InChI: InChI=1S/C12H17NOS/c1-2-4-12(5-3-1)15-11-8-13-6-9-14-10-7-13/h1-5H,6-11H2
Release date: 2020-11-11
FACTOR XIA (C500S [C122S]) IN COMPLEX WITH THE INHIBITOR methyl ~{N}-[4-[2-[(1~{S})-1-[[(~{E})-3-[5-chloranyl-2-(1,2,3,4-tetrazol-1-yl)phenyl]prop-2-enoyl]amino]-2-phenyl-ethyl]pyridin-4-yl]phenyl]carbamate (PDB entry 5EXN)
Macromolecule: Coagulation factor XIa light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 238 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.17
R free: 0.195
Average B factor: 22.98
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 100 MM SODIUM CITRATE, PH 5.0, 36%(w/v) PEG4000
Matthews coefficient: 2.13
Solvent content (%): 42.39
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: 2016-04-13
Crystal structure of CLK1 in complex with macrocycle ODS2003208 (PDB entry 6Z50)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 339 residues
Sequence: SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1508
R free: 0.1795
Average B factor: 22.633
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 23% PEG3350, 0.1M sodium malonate
Matthews coefficient: 2.88
Solvent content (%): 57.35
Ligand: 11,15-dimethyl-6-(oxan-4-yloxy)-8-oxa-2,11,15,19,21,23-hexazatetracyclo[15.6.1.13,7.020,24]pentacosa-1(23),3(25),4,6,17,20(24),21-heptaen-10-one   (Q7K)
Ligand formula: C25 H32 N6 O4
Ligand molecular weight: 480.559
Ligand SMILES: CN1CCCN(C(=O)COc2cc(ccc2OC3CCOCC3)Nc4c5c(c[nH]c5ncn4)C1)C
Ligand InChI: InChI=1S/C25H32N6O4/c1-30-8-3-9-31(2)22(32)15-34-21-12-18(4-5-20(21)35-19-6-10-33-11-7-19)29-25-23-17(14-30)13-26-24(23)27-16-28-25/h4-5,12-13,16,19H,3,6-11,14-15H2,1-2H3,(H2,26,27,28,29)
Release date: 2020-06-03
Crystal structure of BACE complex with BMC013 (PDB entry 5QDA)
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: 0.181
R free: 0.209
Average B factor: 53.85
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 4-FOLD EXCESS OF BMC013 ADDED FROM A 50MM STOCK
SOLUTION IN DMSO (1.4% DMSO IN DROP). CRYO-PROTECTANT WAS 20%(V/V) GLYCEROL, 80% (V/V) RESERVOIR SOLUTION
Matthews coefficient: 3.1
Solvent content (%): 60.28
Ligand: (4S)-4-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-18-methoxy-3,15,17-triazatricyclo[14.3.1.1~6,10~]henicosa-1(20),6(21),7,9,16,18-hexaen-2-one (E74)
Ligand formula: C31 H40 N4 O3
Ligand molecular weight: 516.674
Ligand SMILES: CC(C)c1cccc(c1)CNCC(C2Cc3cccc(c3)CCCCNc4cc(cc(n4)OC)C(=O)N2)O
Ligand InChI: InChI=1S/C31H40N4O3/c1-21(2)25-12-7-11-24(15-25)19-32-20-28(36)27-16-23-10-6-9-22(14-23)8-4-5-13-33-29-17-26(31(37)34-27)18-30(35-29)38-3/h6-7,9-12,14-15,17-18,21,27-28,32,36H,4-5,8,13,16,19-20H2,1-3H3,(H,33,35)(H,34,37)/t27-,28+/m0/s1
Release date: 2020-06-03
BMP1 complexed with a hydroxamate - compound 2 (PDB entry 6BTQ)
Macromolecule: Bone morphogenetic protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.19
Sequence length: 202 residues
Sequence: XAATSRPERVWPDGVIPFVIGGNFTGSQRAVFRQAMRHWEKHTCVTFLERTDEDSYIVFTYRPCGCCSYVGRRGGGPQAISIGKNCDKFGIVVHELGHVVGFWHEHTRPDRDRHVSIVRENIQPGQEYNFLKMEPQEVESLGETYDFDSIMHYARNTFSRGIFLDTIVPKYEVNGVKPPIGQRTRLSKGDIAQARKLYKCPA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1833
R free: 0.2058
Average B factor: 26.366
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 8-12% PEG 3350 150-200mM KSCN 10mM spermidine
Matthews coefficient: 2.67
Solvent content (%): 54
Ligand: THIOCYANATE ION (SCN)
Ligand formula: C N S
Ligand molecular weight: 58.082
Ligand SMILES: C(#N)[S-]
Ligand InChI: InChI=1S/CHNS/c2-1-3/h3H/p-1
Release date: 2018-08-08
SRPK1 in complex with MSC2711186 (PDB entry 7PQS)
Macromolecule: SRSF protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 383 residues
Sequence: SMDPNDYCKGGYHLVKIGDLFNGRYHVIRKLGWGHFSTVWLSWDIQGKKFVAMKVVKSAEHYTETALDEIRLLKSVRNSDPNDPNREMVVQLLDDFKISGVNGTHICMVFEVLGHHLLKWIIKSNYQGLPLPCVKKIIQQVLQGLDYLHTKCRIIHTDIKPENILLSVNEQYIRRLAAEATEWQRSGAPPPSGSAVSTAPATAGNFLVNPLEPKNAEKLKVKIADLGNACWVHKHFTEDIQTRQYRSLEVLIGSGYNTPADIWSTACMAFELATGDYLFEPHSGEEYTRDEDHIALIIELLGKVPRKLIVAGKYSKEFFTKKGDLKHITKLKPWGLFEVLVEKYEWSQEEAAGFTDFLLPMLELIPEKRATAAECLRHPWLNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.199
R free: 0.2356
Average B factor: 41.631
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 278
Crystal growth procedure: 15% PEG Smear Broad, 0.1M cacodylate, 5% tacsimate, 10% ethylene glycol
Matthews coefficient: 2.89
Solvent content (%): 57.5
Ligand: ~{N}-[3-[[[2-(6-chloranyl-7-fluoranyl-1~{H}-benzimidazol-2-yl)pyrimidin-4-yl]amino]methyl]pyridin-2-yl]-~{N}-methyl-methanesulfonamide (80H)
Ligand formula: C19 H17 Cl F N7 O2 S
Ligand molecular weight: 461.9
Ligand SMILES: CN(c1c(cccn1)CNc2ccnc(n2)c3[nH]c4c(n3)ccc(c4F)Cl)S(=O)(=O)C
Ligand InChI: InChI=1S/C19H17ClFN7O2S/c1-28(31(2,29)30)19-11(4-3-8-23-19)10-24-14-7-9-22-17(26-14)18-25-13-6-5-12(20)15(21)16(13)27-18/h3-9H,10H2,1-2H3,(H,25,27)(H,22,24,26)
Release date: 2021-12-15
HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) complexed with HEPES (PDB entry 8TK5)
Macromolecule: Dual specificity protein phosphatase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 183 residues
Sequence: GSFELSVQDLNDLLSDGSGCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVNTNANFYKDSGITYLGIKANDTQEFNLSAYFERAADFIDQALAQKNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNREIGPNDGFLAQLCQLNDRLAKEGKLKP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.14695
R free: 0.19124
Average B factor: 19.955
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: Protein in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA was mixed with the precipitant solution (100 mM HEPES pH7.5, 50 mM NH4F, 28% (w/v) PEG 4K) and equilibrated against the precipitant solution.
Matthews coefficient: 2.2
Solvent content (%): 44.02
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: 2024-08-14
The crystal structure of upain-1-W3A in complex with uPA at pH7.4 (PDB entry 4ZKO)
Macromolecule: Urokinase-type plasminogen activator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 247 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.21026
R free: 0.22497
Average B factor: 16.784
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 298
Crystal growth procedure: 50 mM sodium citrate pH 4.6, 2.0 M ammonium sulfate supplemented with 5% PEG 400
Matthews coefficient: 2.14
Solvent content (%): 42.61
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: 2016-05-18
Human CYP3A4 bound to an inhibitor (PDB entry 6DAB)
Macromolecule: Cytochrome P450 3A4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14
Sequence length: 487 residues
Sequence: MAYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDGTVSGAHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.2149
R free: 0.2698
Crystallization method: MICROBATCH
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: peg 3350, malonate
Matthews coefficient: 2.21
Solvent content (%): 44.24
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2019-04-03