satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of Trk-A complexed with a selective inhibitor CH7057288 (PDB entry 5WR7)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 304 residues
Sequence: HIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.76
R work: 0.20634
R free: 0.23434
Average B factor: 40.719
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.05-0.15M KH2PO4, 0.1M MES pH 6.25, 1.5-2.5M NaCl, 0.05-0.15M NaH2PO4, 0.01M TCEP HCl
Matthews coefficient: 3.11
Solvent content (%): 60.52
Ligand: N-tert-butyl-2-[2-[6,6-dimethyl-8-(methylsulfonylamino)-11-oxidanylidene-naphtho[2,3-b][1]benzofuran-3-yl]ethynyl]-6-methyl-pyridine-4-carboxamide (RCH)
Ligand formula: C32 H31 N3 O5 S
Ligand molecular weight: 569.671
Ligand SMILES: Cc1cc(cc(n1)C#Cc2ccc3c(c2)oc4c3C(=O)c5ccc(cc5C4(C)C)NS(=O)(=O)C)C(=O)NC(C)(C)C
Ligand InChI: InChI=1S/C32H31N3O5S/c1-18-14-20(30(37)34-31(2,3)4)16-21(33-18)10-8-19-9-12-24-26(15-19)40-29-27(24)28(36)23-13-11-22(35-41(7,38)39)17-25(23)32(29,5)6/h9,11-17,35H,1-7H3,(H,34,37)
Release date: 2017-12-06
CRYSTAL STRUCTURE OF JANUS KINASE 2 IN COMPLEX WITH A 9H-CARBAZOLE-1-CARBOXAMIDE INHIBITOR (PDB entry 4ZIM)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 321 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMRDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.202
R free: 0.2742
Average B factor: 38
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 100mM MES buffer, 100mM NaCl, 28% (w/v) PEG3350, 2mM DTT and 200mM tri-sodium citrate
Matthews coefficient: 2.95
Solvent content (%): 58.34
Ligand: 3-(3,4-dichlorophenyl)-6-(morpholin-4-ylcarbonyl)-9H-carbazole-1-carboxamide (4OK)
Ligand formula: C24 H19 Cl2 N3 O3
Ligand molecular weight: 468.332
Ligand SMILES: c1cc(c(cc1c2cc3c4cc(ccc4[nH]c3c(c2)C(=O)N)C(=O)N5CCOCC5)Cl)Cl
Ligand InChI: InChI=1S/C24H19Cl2N3O3/c25-19-3-1-13(12-20(19)26)15-10-17-16-9-14(24(31)29-5-7-32-8-6-29)2-4-21(16)28-22(17)18(11-15)23(27)30/h1-4,9-12,28H,5-8H2,(H2,27,30)
Release date: 2015-06-03
The crystal structure of CK2alpha in complex with compound 32 (PDB entry 6EHU)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 342 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.189
R free: 0.218
Average B factor: 40.76
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.11
Solvent content (%): 41.84
Ligand: 2-(1~{H}-benzimidazol-2-yl)-~{N}-[[4-(2-ethylphenyl)-3-(trifluoromethyl)phenyl]methyl]ethanamine (B5E)
Ligand formula: C25 H24 F3 N3
Ligand molecular weight: 423.473
Ligand SMILES: CCc1ccccc1c2ccc(cc2C(F)(F)F)CNCCc3[nH]c4ccccc4n3
Ligand InChI: InChI=1S/C25H24F3N3/c1-2-18-7-3-4-8-19(18)20-12-11-17(15-21(20)25(26,27)28)16-29-14-13-24-30-22-9-5-6-10-23(22)31-24/h3-12,15,29H,2,13-14,16H2,1H3,(H,30,31)
Release date: 2018-02-28
Crystal structure of TL10-81 bound to TAK1-TAB1 (PDB entry 5E7R)
Macromolecule: TAK1 kinase - TAB1 chimera fusion protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 314 residues
Sequence: SLHMIDYKEIEVEEVVGRGAFGVVCKAKWRAKDVAIKQIESESERKAFIVELRQLSRVNHPNIVKLYGACLNPVCLVMEYAEGGSLYNVLHGAEPLPYYTAAHAMSWCLQCSQGVAYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICDFGTACDIQTHMTNNKGSAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDEIGGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQHSLPPGEDGRVEPYVDFAEFYRLWSVDHGEQSVVTAP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.22
R free: 0.2456
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.65-0.75 M sodium citrate pH 7.0, 0.2 M NaCl, 0.1 M Tris pH 7.0, and 5mM adenosine. Adenosine bound TAK1-TAB1 crystals are backsoaked with inhibitor
Matthews coefficient: 4.07
Solvent content (%): 69.77
Ligand: 2-chloro-N-{2-[(5-chloro-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)oxy]phenyl}acetamide (5KW)
Ligand formula: C23 H24 Cl2 N6 O2
Ligand molecular weight: 487.382
Ligand SMILES: CN1CCN(CC1)c2ccc(cc2)Nc3ncc(c(n3)Oc4ccccc4NC(=O)CCl)Cl
Ligand InChI: InChI=1S/C23H24Cl2N6O2/c1-30-10-12-31(13-11-30)17-8-6-16(7-9-17)27-23-26-15-18(25)22(29-23)33-20-5-3-2-4-19(20)28-21(32)14-24/h2-9,15H,10-14H2,1H3,(H,28,32)(H,26,27,29)
Release date: 2016-09-21
Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues (PDB entry 5AQQ)
Macromolecule: HEAT SHOCK COGNATE 71 KDA PROTEIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.51
Sequence length: 386 residues
Sequence: GPLGSMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.72
R work: 0.1952
R free: 0.2409
Average B factor: 57.59
Crystallization pH: 8.5
Crystal growth procedure: 16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL
Matthews coefficient: 2.46
Solvent content (%): 49.94
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: 2016-10-05
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B25 (PDB entry 7THC)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 163 residues
Sequence: NPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1339
R free: 0.1635
Average B factor: 13.25
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 13% PEG 3350
0.5 M KH2PO4
7.5% glycerol
Protein and inhibitor were mixed in ratio 1:2
1 uL of protein:inhibitor complex was mixed with 1 uL mother liquor
Matthews coefficient: 2.56
Solvent content (%): 51.98
Ligand: 3-(4'-{[(4S,7S,11R,13E,19S)-19-{[2-(2-aminoethoxy)ethyl]carbamoyl}-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosin-4-yl]methyl}[1,1'-biphenyl]-4-yl)prop-2-ynoic acid (I4Z)
Ligand formula: C52 H57 N7 O9
Ligand molecular weight: 924.05
Ligand SMILES: c1ccc(cc1)CC23CCCN(C2)C(=O)C=CC(=O)NCCC(NC(=O)Cc4ccccc4CNC(=O)C(NC3=O)Cc5ccc(cc5)c6ccc(cc6)C#CC(=O)O)C(=O)NCCOCCN
Ligand InChI: InChI=1S/C52H57N7O9/c53-25-29-68-30-27-55-49(65)43-23-26-54-45(60)20-21-47(62)59-28-6-24-52(35-59,33-38-7-2-1-3-8-38)51(67)58-44(50(66)56-34-42-10-5-4-9-41(42)32-46(61)57-43)31-37-13-18-40(19-14-37)39-16-11-36(12-17-39)15-22-48(63)64/h1-5,7-14,16-21,43-44H,6,23-35,53H2,(H,54,60)(H,55,65)(H,56,66)(H,57,61)(H,58,67)(H,63,64)/b21-20+/t43-,44-,52-/m0/s1
Release date: 2022-08-24
CRAF ras-binding domain chimera, apo form (PDB entry 8JNA)
Macromolecule: RAF proto-oncogene serine/threonine-protein kinase, CRaf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 94 residues
Sequence: GPLGSDPSKTSNTIRVFLPNSQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVYRLQDGEKKPIGWNTDAAWLIGEELQVEFLDHVPLTTHNF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2515
R free: 0.2717
Average B factor: 41.79
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 1.0M tri-sodium citrate, 0.1M imidazole, pH 8.0
Matthews coefficient: 1.91
Solvent content (%): 35.73
Release date: 2024-06-19
Anaplastic Lymphoma Kinase with a novel carboline inhibitor (PDB entry 8ARJ)
Macromolecule: ALK tyrosine kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 321 residues
Sequence: GSNPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVEEEEKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.645
R work: 0.1966
R free: 0.2287
Average B factor: 40.512
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 286
Crystal growth procedure: 0.15 M ammonium sulphate, 9-10.5% monomethyl ether poly (ethylene glycol) (MW 5000), and 0.1 M MES buffer pH 5.3 - 5.6
Matthews coefficient: 2.1
Solvent content (%): 41.34
Ligand: 3-(dimethylamino)-1-[3-[4-(4-methylpiperazin-1-yl)phenyl]-9~{H}-pyrido[2,3-b]indol-6-yl]prop-2-en-1-one (NRR)
Ligand formula: C27 H29 N5 O
Ligand molecular weight: 439.552
Ligand SMILES: CN1CCN(CC1)c2ccc(cc2)c3cc4c5cc(ccc5[nH]c4nc3)C(=O)C=CN(C)C
Ligand InChI: InChI=1S/C27H29N5O/c1-30(2)11-10-26(33)20-6-9-25-23(16-20)24-17-21(18-28-27(24)29-25)19-4-7-22(8-5-19)32-14-12-31(3)13-15-32/h4-11,16-18H,12-15H2,1-3H3,(H,28,29)/b11-10-
Release date: 2022-09-14
Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4-ol (PDB entry 5IVF)
Macromolecule: Lysine-specific demethylase 5A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.683
R work: 0.1688
R free: 0.2017
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4,
0.1 M Tris-HCl (pH 8.6-9.2)
0-20% glycerol 
25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.22
Solvent content (%): 44.71
Ligand: 8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4-ol (6EB)
Ligand formula: C15 H14 F3 N5 O2
Ligand molecular weight: 353.299
Ligand SMILES: Cn1cc(nc1)c2c3c(ccn2)c(nc(n3)OCCCC(F)(F)F)O
Ligand InChI: InChI=1S/C15H14F3N5O2/c1-23-7-10(20-8-23)12-11-9(3-5-19-12)13(24)22-14(21-11)25-6-2-4-15(16,17)18/h3,5,7-8H,2,4,6H2,1H3,(H,21,22,24)
Release date: 2016-07-27
JmjC domain-containing protein 5 (JMJD5) in complex with Mn and L-2-hydroxyglutarate (PDB entry 6I9N)
Macromolecule: JmjC domain-containing protein 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.27
Sequence length: 256 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPCMQKWSLEYIQEIAGCRTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYCSLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSCILSPGEILFIPVKYWHYVRALDLSFSVSFWWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.361
R work: 0.1496
R free: 0.1589
Average B factor: 22
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Bis-Tris pH 6.5, 15.0 % PEG3350, 0.002 M MnCl2
Matthews coefficient: 2.33
Solvent content (%): 47.33
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: 2019-12-04
Crystal structure of G6PD in complex with structural NADP (PDB entry 6E08)
Macromolecule: Glucose-6-phosphate 1-dehydrogenase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.49
Sequence length: 515 residues
Sequence: MAEQVALSRTQVCGILREELFQGDAFHQSDTHIFIIMGASGDLAKKKIYPTIWWLFRDGLLPENTFIVGYARSRLTVADIRKQSEPFFKATPEEKLKLEDFFARNSYVAGQYDDAASYQRLNSHMNALHLGSQANRLFYLALPPTVYEAVTKNIHESCMSQIGWNRIIVEKPFGRDLQSSDRLSNHISSLFREDQIYRIDHYLGKEMVQNLMVLRFANRIFGPIWNRDNIACVILTFKEPFGTEGRGGYFDEFGIIRDVMQNHLLQMLCLVAMEKPASTNSDDVRDEKVKVLKCISEVQANNVVLGQYVGNPDGEGEATKGYLDDPTVPRGSTTATFAAVVLYVENERWDGVPFILRCGKALNERKAEVRLQFHDVAGDIFHQQCKRNELVIRVQPNEAVYTKMMTKKPGMFFNPEESELDLTYGNRYKNVKLPDAYERLILDVFCGSQMHFVRSDELREAWRIFTPLLHQIELEKPKPIPYIYGSRGPTEADELMKRVGFQYEGTYKWVNPHKL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.17182
R free: 0.21258
Average B factor: 24.422
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 293
Crystal growth procedure: 20% w/v PEG 3350, 0.2 M potassium formate
Matthews coefficient: 2.39
Solvent content (%): 48.52
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2018-07-25
Carbonic Anhydrase II in complex with the alkyl ureas 3g (PDB entry 8FQX)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.496
R work: 0.1711
R free: 0.191
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris base
Matthews coefficient: 2.02
Solvent content (%): 39.08
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: 2023-02-01
Crystal structure of Thrombin in complex with macrocycle T1 (PDB entry 8ASF)
Macromolecule: Thrombin light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58
R work: 0.195
R free: 0.24
Average B factor: 41.458
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM sodium acetate, 50 mM magnesium chloride hexahydrate, 8% w/v PEG
3350, pH 4.5
Matthews coefficient: 2.86
Solvent content (%): 56.95
Ligand: 5-chloranyl-~{N}-[[(9~{S},15~{R})-8,14,17-tris(oxidanylidene)-3,20-dithia-7,13,16-triazatetracyclo[20.2.2.1^{5,7}.1^{9,13}]octacosa-1(25),22(26),23-trien-15-yl]methyl]thiophene-2-carboxamide (NWF)
Ligand formula: C29 H35 Cl N4 O4 S3
Ligand molecular weight: 635.261
Ligand SMILES: c1cc2ccc1CSCCC(=O)NC(C(=O)N3CCCC(C3)C(=O)N4CC(C4)CSC2)CNC(=O)c5ccc(s5)Cl
Ligand InChI: InChI=1S/C29H35ClN4O4S3/c30-25-8-7-24(41-25)27(36)31-12-23-29(38)33-10-1-2-22(15-33)28(37)34-13-21(14-34)18-40-17-20-5-3-19(4-6-20)16-39-11-9-26(35)32-23/h3-8,21-23H,1-2,9-18H2,(H,31,36)(H,32,35)/t22-,23+/m0/s1
Release date: 2024-03-06
Crystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal domain of its neuronal receptor SV2C (PDB entry 5MOY)
Macromolecule: Botulinum neurotoxin type A
Type: Protein, polypeptide(L)
Source organism: Clostridium botulinum
EC number: 3.4.24.69
Sequence length: 428 residues
Sequence: GSKNIVNTSILSIVYKKDDLIDLSRYGAKINIGDRVYYDSIDKNQIKLINLESSTIEVILKNAIVYNSMYENFSTSFWIKIPKYFSKINLNNEYTIINCIENNSGWKVSLNYGEIIWTLQDNKQNIQRVVFKYSQMVNISDYINRWIFVTITNNRLTKSKIYINGRLIDQKPISNLGNIHASNKIMFKLDGCRDPRRYIMIKYFNLFDKELNEKEIKDLYDSQSNSGILKDFWGNYLQYDKPYYMLNLFDPNKYVDVNNIGIRGYMYLKGPRGSVVTTNIYLNSTLYEGTKFIIKKYASGNEDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKDDQGIRNKCKMNLQDNNGNDIGFIGFHLYDNIAKLVASNWYNRQVGKASRTFGCSWEFIPVDDGWGESSL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.302
R work: 0.1947
R free: 0.2512
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 285
Crystal growth procedure: 20% PEG 8000, 65 mM Hepes
Matthews coefficient: 2.63
Solvent content (%): 53.23
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: 2017-03-15
Crystal structure of human Casein Kinase I delta in complex with compound 31b (PDB entry 6F26)
Macromolecule: Casein kinase I isoform delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 314 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.1895
R free: 0.2087
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 5.5, 10 % (w/v) PEG 4000, 0.2 M lithium sulfate
Matthews coefficient: 2.53
Solvent content (%): 51.4
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: 2019-03-13
Human Cytochrome P450 17A1 in complex with inhibitor: abiraterone C6 nitrile (PDB entry 6CIZ)
Macromolecule: Steroid 17-alpha-hydroxylase/17,20 lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.19
Sequence length: 494 residues
Sequence: MAKKTGAKYPKSLLSLPLVGSLPFLPRHGHMHNNFFKLQKKYGPIYSVRMGTKTTVIVGHHQLAKEVLIKKGKDFSGRPQMATLDIASNNRKGIAFADSGAHWQLHRRLAMATFALFKDGDQKLEKIICQEISTLCDMLATHNGQSIDISFPVFVAVTNVISLICFNTSYKNGDPELNVIQNYNEGIIDNLSKDSLVDLVPWLKIFPNKTLEKLKSHVKIRNDLLNKILENYKEKFRSDSITNMLDTLMQAKMNSDNGNAGPDQDSELLSDNHILTTIGDIFGAGVETTTSVVKWTLAFLLHNPQVKKKLYEEIDQNVGFSRTPTISDRNRLLLLEATIREVLRLRPVAPMLIPHKANVDSSIGEFAVDKGTEVIINLWALHHNEKEWHQPDQFMPERFLNPAGTQLISPSVSYLPFGAGPRSCIGEILARQELFLIMAWLLQRFDLEVPDDGQLPSLEGIPKVVFLIDSFKVKIKVRQAWREAQAEGSTHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.601
R work: 0.1849
R free: 0.243
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.175 M Tris, pH 8.5 containing 35% PEG 3350, 3% glycerol, and 0.250-0.275 M lithium sulfate
Matthews coefficient: 2.6
Solvent content (%): 52.77
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: 2018-06-06
DYRK1A in complex with JWD-065 (PDB entry 6EIV)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 368 residues
Sequence: GASDSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADEGTNTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.1965
R free: 0.2355
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M KSCN; 0.05M LiCl; 10% PEG 3350, pH 6.8
Matthews coefficient: 2.66
Solvent content (%): 53.78
Ligand: ~{N}-[3-[[4-azanyl-2-[[4-(4-methylpiperazin-1-yl)phenyl]amino]-1,3-thiazol-5-yl]carbonyl]phenyl]propanamide (B6Q)
Ligand formula: C24 H28 N6 O2 S
Ligand molecular weight: 464.583
Ligand SMILES: CCC(=O)Nc1cccc(c1)C(=O)c2c(nc(s2)Nc3ccc(cc3)N4CCN(CC4)C)N
Ligand InChI: InChI=1S/C24H28N6O2S/c1-3-20(31)26-18-6-4-5-16(15-18)21(32)22-23(25)28-24(33-22)27-17-7-9-19(10-8-17)30-13-11-29(2)12-14-30/h4-10,15H,3,11-14,25H2,1-2H3,(H,26,31)(H,27,28)
Release date: 2018-08-29