satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to pyridin-benzenesulfonamide inhibitor (PDB entry 6NCG)
Macromolecule: Serine/threonine-protein kinase VRK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 324 residues
Sequence: SMPFPEGKVLDDMEGNQWVLGKKIGSGGFGLIYLAFPTNKPEKDARHVVKVEYQENGPLFSELKFYQRVAKKDCIKKWIERKQLDYLGIPLFYGSGLTEFKGRSYRFMVMERLGIDLQKISGQNGTFKKSTVLQLGIRMLDVLEYIHENEYVHGDIKAANLLLGYKNPDQVYLADYGLSYRYCPNGNHKQYQENPRKGHNGTIEFTSLDAHKGVALSRRSDVEILGYCMLRWLCGKLPWEQNLKDPVAVQTAKTNLLDELPQSVLKWAPSGSSCCEIAQFLVCAHSLAYDEKPNYQALKKILNPHGIPLGPLDFSTKGQSINVH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.22061
R free: 0.29694
Average B factor: 65.063
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 27.5% PEG3350; 200 mM LiSO4; 0.1M SBG (each Sodium-tartrate + Bis-Tris + Glycylglycine) pH 6.0
Matthews coefficient: 2.15
Solvent content (%): 42.71
Ligand: 4-[6-amino-5-(3,5-difluoro-4-hydroxyphenyl)pyridin-3-yl]benzene-1-sulfonamide (KJD)
Ligand formula: C17 H13 F2 N3 O3 S
Ligand molecular weight: 377.365
Ligand SMILES: c1cc(ccc1c2cc(c(nc2)N)c3cc(c(c(c3)F)O)F)S(=O)(=O)N
Ligand InChI: InChI=1S/C17H13F2N3O3S/c18-14-6-10(7-15(19)16(14)23)13-5-11(8-22-17(13)20)9-1-3-12(4-2-9)26(21,24)25/h1-8,23H,(H2,20,22)(H2,21,24,25)
Release date: 2019-01-16
Crystal structure of the KH1 domain of human RNA-binding E3 ubiquitin-protein ligase MEX-3C complex with RNA (PDB entry 5WWW)
Macromolecule: RNA-binding E3 ubiquitin-protein ligase MEX3C
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 94 residues
Sequence: GHHHHHHMQAALLRRKSVNTTECVPVPSSEHVAEIVGRQGCKIKALRAKTNTYIKTPVRGEEPIFVVTGRKEDVAMAKREILSAAEHFSMIRAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.798
R work: 0.172
R free: 0.2091
Average B factor: 26.3348
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 5% v/v Tacsimate pH 7.0, 0.1M HEPES pH 7.0, 10% w/v polyethylene glycol monomethyl ether 2000
Matthews coefficient: 2.47
Solvent content (%): 50.19
Release date: 2017-08-23
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z1170065264 (PDB entry 5QP2)
Macromolecule: DCP2 (NUDT20)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.62
Sequence length: 167 residues
Sequence: SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLARLYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGFSSTGSTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.1931
R free: 0.2501
Average B factor: 45.942
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M acetate, pH 4.5, 5-25% PEG3350
Matthews coefficient: 2.48
Solvent content (%): 50.45
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: 2019-05-08
CLK3 bound with benzothiazole Tg003 (Cpd 2) (PDB entry 6YTW)
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): 2.0
R work: 0.1839
R free: 0.2269
Average B factor: 33.782
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 21% PEG 3350, 0,2M Na/K PO4, 10% Ethylene Glycol
Matthews coefficient: 2.95
Solvent content (%): 58.26
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
CDK2 liganded with ATP and Mg2+ (PDB entry 8FP5)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1942
R free: 0.2304
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 10% PEG 3350, 10% ethylene glycol, 50mM HEPES, pH 7.5
Matthews coefficient: 2.04
Solvent content (%): 39.71
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2023-05-31
Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric ligand FGC3337 (PDB entry 9EPZ)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 338 residues
Sequence: SMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.21273
R free: 0.24473
Average B factor: 49.465
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M bis-tris pH 5.5 
23-26% (v/v) PEG 3350 
0.2 M ammonia sulphate
Matthews coefficient: 3.16
Solvent content (%): 61.04
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: 2024-05-01
Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10 (PDB entry 7Q43)
Macromolecule: Dedicator of cytokinesis protein 10 peptide
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 25 residues
Sequence: KLPSHSFEIDHEDADKDEDTTSHSS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4000234708
R work: 0.202444119505
R free: 0.264969422568
Average B factor: 38.167441888
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293.15
Crystal growth procedure: hanging drop
20% PEG 3350
0.18M tris amonium citrate
Matthews coefficient: 3.01
Solvent content (%): 59.15
Ligand: CITRIC ACID (CIT)
Ligand formula: C6 H8 O7
Ligand molecular weight: 192.124
Ligand SMILES: C(C(=O)O)C(CC(=O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)
Release date: 2022-11-16
JAK2 JH1 in complex with PN4-014 (PDB entry 6VNJ)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 308 residues
Sequence: HHHHHHHHENLYFQGDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1847
R free: 0.211
Average B factor: 50.9264
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% PEG 3350
Matthews coefficient: 3.04
Solvent content (%): 59.58
Ligand: 3-[4-(2-{[4-(piperidin-4-yl)phenyl]amino}-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile (R5S)
Ligand formula: C23 H26 N8
Ligand molecular weight: 414.506
Ligand SMILES: c1cc(ccc1C2CCNCC2)Nc3nc(c4c(n3)NCC4)c5cnn(c5)CCC#N
Ligand InChI: InChI=1S/C23H26N8/c24-9-1-13-31-15-18(14-27-31)21-20-8-12-26-22(20)30-23(29-21)28-19-4-2-16(3-5-19)17-6-10-25-11-7-17/h2-5,14-15,17,25H,1,6-8,10-13H2,(H2,26,28,29,30)
Release date: 2021-02-17
Thrombin in complex with (S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-D-arginyl)pyrrolidine-2-carboxamide (PDB entry 5JFD)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.13
R free: 0.1633
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM Sodium dihydrogen phosphate ph 7.5, 
350 mM NACl, 27% PEG 8000,
Matthews coefficient: 2.5
Solvent content (%): 51.38
Ligand: (2S)-N-[[2-(aminomethyl)-5-chloro-phenyl]methyl]-1-[(2R)-5-carbamimidamido-2-(phenylmethylsulfonylamino)pentanoyl]pyrrolidine-2-carboxamide (2TS)
Ligand formula: C26 H36 Cl N7 O4 S
Ligand molecular weight: 578.127
Ligand SMILES: c1ccc(cc1)CS(=O)(=O)NC(CCCNC(=N)N)C(=O)N2CCCC2C(=O)NCc3cc(ccc3CN)Cl
Ligand InChI: InChI=1S/C26H36ClN7O4S/c27-21-11-10-19(15-28)20(14-21)16-32-24(35)23-9-5-13-34(23)25(36)22(8-4-12-31-26(29)30)33-39(37,38)17-18-6-2-1-3-7-18/h1-3,6-7,10-11,14,22-23,33H,4-5,8-9,12-13,15-17,28H2,(H,32,35)(H4,29,30,31)/t22-,23+/m1/s1
Release date: 2017-05-24
Crystal structure of DYRK1A in complex with RD0448 (PDB entry 7FHT)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 361 residues
Sequence: GSSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.18843
R free: 0.24938
Average B factor: 61.619
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100mM BIS-TRIS propane, 200 mM Sodium fluoride, 22% PEG3350, pH 8.0
Matthews coefficient: 2.72
Solvent content (%): 54.73
Ligand: (5~{Z})-5-[(3-ethynyl-4-methoxy-phenyl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one (4WD)
Ligand formula: C13 H9 N O2 S2
Ligand molecular weight: 275.346
Ligand SMILES: COc1ccc(cc1C#C)C=C2C(=O)NC(=S)S2
Ligand InChI: InChI=1S/C13H9NO2S2/c1-3-9-6-8(4-5-10(9)16-2)7-11-12(15)14-13(17)18-11/h1,4-7H,2H3,(H,14,15,17)/b11-7-
Release date: 2022-03-23
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000240a (PDB entry 5QEE)
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): 1.932
R work: 0.2009
R free: 0.2292
Average B factor: 46.0529
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: 3.26
Solvent content (%): 62.23
Ligand: 3-cyclopentyl-N-(5-methyl-1,3-thiazol-2-yl)propanamide (JJ4)
Ligand formula: C12 H18 N2 O S
Ligand molecular weight: 238.349
Ligand SMILES: Cc1cnc(s1)NC(=O)CCC2CCCC2
Ligand InChI: InChI=1S/C12H18N2OS/c1-9-8-13-12(16-9)14-11(15)7-6-10-4-2-3-5-10/h8,10H,2-7H2,1H3,(H,13,14,15)
Release date: 2018-10-10
Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating A and incorporated 8-oxo-dGMP (PDB entry 4X5V)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 325 residues
Sequence: NHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.2144
R free: 0.245
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 0.1 M sodium citrate pH 5.6 and 1 M ammonium phosphate monobasic
Matthews coefficient: 2.89
Solvent content (%): 57.4
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2015-10-28
the structure of mini-MFN1 K88A in complex with GDP (PDB entry 5GNR)
Macromolecule: Mitofusin-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 421 residues
Sequence: MAEPVSPLKHFVLAKKAITAIFDQLLEFVTEGSHFVEATYKNPELDRIATEDDLVEMQGYKDKLSIIGEVLSRRHMKVAFFGRTSSGASSVINAMLWDKVLPSGIGHITNCFLSVEGTDGDKAYLMTEGSDEKKSVKTVNQLAHALHMDKDLKAGCLVRVFWPKAKCALLRDDLVLVDSPGTDVTTELDSWIDKFCLDADVFVLVANSESTLMNTEKHFFHKVNERLSKPNIFILNNRWDASASEPEYMEDVRRQHMERCLHFLVEELKVVNALEAQNRIFFVSAKEVLSARKQKAQGMPESGVALAEGFHARLQEFQNFEQIFEECISQSAVKTKFEQHTIRAKQILATVKNIMDSVNLAAEDGSGSGSGGSEIARLPKEIDQLEKIQNNSKLLRNKAVQLENELENFTKQFLPSSNEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2163
R free: 0.3016
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 200 mM ammonium fluoride, 20% (w/v) PEG 3350
Matthews coefficient: 2.67
Solvent content (%): 53.9
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: 2016-11-23
Crystal structure of human WEE1 kinase domain in complex with ZN-c3 (PDB entry 7N3U)
Macromolecule: Wee1-like protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 285 residues
Sequence: MKSRYTTEFHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALREVYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDLLLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGHVTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEIRQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVLLSASRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2169
R free: 0.2668
Average B factor: 71.916
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291.15
Crystal growth procedure: 20% PEG 20K
Matthews coefficient: 2.16
Solvent content (%): 42.94
Ligand: 1-[(7R)-7-ethyl-7-hydroxy-6,7-dihydro-5H-cyclopenta[b]pyridin-2-yl]-6-[4-(4-methylpiperazin-1-yl)anilino]-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one (05J)
Ligand formula: C29 H34 N8 O2
Ligand molecular weight: 526.633
Ligand SMILES: CCC1(CCc2c1nc(cc2)N3c4c(cnc(n4)Nc5ccc(cc5)N6CCN(CC6)C)C(=O)N3CC=C)O
Ligand InChI: InChI=1S/C29H34N8O2/c1-4-14-36-27(38)23-19-30-28(31-21-7-9-22(10-8-21)35-17-15-34(3)16-18-35)33-26(23)37(36)24-11-6-20-12-13-29(39,5-2)25(20)32-24/h4,6-11,19,39H,1,5,12-18H2,2-3H3,(H,30,31,33)/t29-/m1/s1
Release date: 2021-09-01
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434909 (PDB entry 5RXG)
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): 1.52
R work: 0.1759
R free: 0.2062
Average B factor: 18.871
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: 2.06
Solvent content (%): 40.26
Ligand: (2S)-1-{[(2,6-dichlorophenyl)methyl]amino}propan-2-ol (WLD)
Ligand formula: C10 H13 Cl2 N O
Ligand molecular weight: 234.122
Ligand SMILES: CC(CNCc1c(cccc1Cl)Cl)O
Ligand InChI: InChI=1S/C10H13Cl2NO/c1-7(14)5-13-6-8-9(11)3-2-4-10(8)12/h2-4,7,13-14H,5-6H2,1H3/t7-/m0/s1
Release date: 2020-11-11
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster14 (PDB entry 7GU6)
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): 1.56
R work: 0.1978
R free: 0.2181
Average B factor: 39.5554
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.31
Solvent content (%): 62.8
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: 2024-01-31
Crystal structure of the human METTL3-METTL14 complex with compound UOZ097 (PDB entry 7OEL)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1866
R free: 0.213
Average B factor: 33.27
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.15
Solvent content (%): 42.85
Ligand: ~{N}-[[(3~{R})-1-[6-(3~{H}-benzimidazol-4-ylmethylamino)pyrimidin-4-yl]-3-oxidanyl-piperidin-3-yl]methyl]-4-[(4,4-dimethylpiperidin-1-yl)methyl]benzamide (VA8)
Ligand formula: C33 H42 N8 O2
Ligand molecular weight: 582.739
Ligand SMILES: CC1(CCN(CC1)Cc2ccc(cc2)C(=O)NCC3(CCCN(C3)c4cc(ncn4)NCc5cccc6c5[nH]cn6)O)C
Ligand InChI: InChI=1S/C33H42N8O2/c1-32(2)12-15-40(16-13-32)19-24-7-9-25(10-8-24)31(42)35-20-33(43)11-4-14-41(21-33)29-17-28(37-23-38-29)34-18-26-5-3-6-27-30(26)39-22-36-27/h3,5-10,17,22-23,43H,4,11-16,18-21H2,1-2H3,(H,35,42)(H,36,39)(H,34,37,38)/t33-/m1/s1
Release date: 2021-10-20
Crystal structure of GDP-bound human RalA (PDB entry 6P0J)
Macromolecule: Ras-related protein Ral-A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 186 residues
Sequence: MAANKPKGQNSLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTAGQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAEQWNVNYVETSAKTRANVDKVFFDLMREIRARLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.31
R work: 0.1201
R free: 0.156
Average B factor: 17.76
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M calcium acetate, pH 5.5, 18-22% PEG3350
Matthews coefficient: 2.21
Solvent content (%): 44.23
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: 2020-03-04