satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of human cyclic GMP-AMP synthase in complex with phosphate (PDB entry 7FUH)
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): 1.944
R work: 0.1889
R free: 0.2503
Average B factor: 59.0069
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: 1.98
Solvent content (%): 37.99
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2024-02-21
Structure-based Design, Synthesis, and Biological Evaluation of Imidazo[1,2-b]pyridazine-based p38 MAP Kinase Inhibitors (PDB entry 6ANL)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 365 residues
Sequence: GAMGSMSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKSQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDSELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.2058
R free: 0.2634
Average B factor: 37.713
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 15.% PEG 8000, 0.08M NP_HEPES, 0.02M NP_HEPES_Na
Matthews coefficient: 2.17
Solvent content (%): 43.35
Ligand: TAK-715 (T75)
Ligand formula: C24 H21 N3 O S
Ligand molecular weight: 399.508
Ligand SMILES: CCc1nc(c(s1)c2ccnc(c2)NC(=O)c3ccccc3)c4cccc(c4)C
Ligand InChI: InChI=1S/C24H21N3OS/c1-3-21-27-22(18-11-7-8-16(2)14-18)23(29-21)19-12-13-25-20(15-19)26-24(28)17-9-5-4-6-10-17/h4-15H,3H2,1-2H3,(H,25,26,28)
Release date: 2018-01-17
Structure of Cyclophilin A in complex with benzenesulfonohydrazide. (PDB entry 4N1R)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.16975
R free: 0.22331
Average B factor: 25.663
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: Tris, PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2.77
Solvent content (%): 55.6
Ligand: benzenesulfonohydrazide (WM3)
Ligand formula: C6 H8 N2 O2 S
Ligand molecular weight: 172.205
Ligand SMILES: c1ccc(cc1)S(=O)(=O)NN
Ligand InChI: InChI=1S/C6H8N2O2S/c7-8-11(9,10)6-4-2-1-3-5-6/h1-5,8H,7H2
Release date: 2015-08-12
Human Erk2 with an Erk1/2 inhibitor (PDB entry 5NHV)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 381 residues
Sequence: MHHHHHHGGGENLYFQGSHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNLNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRSLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1828
R free: 0.2283
Average B factor: 37.64
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 30% PegMME2K, 100mM HEPES pH 7.6, 200mM Ammonium sulfate
Matthews coefficient: 2.25
Solvent content (%): 45.23
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: 2017-04-19
Crystal structure of Protein Phosphatase 1 in complex with PP1-binding peptide from PTG (PDB entry 7QFB)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 299 residues
Sequence: GHMGSLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1593
R free: 0.1914
Average B factor: 38.6283
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M Lithium sulfate, 1.4 M sodium malonate
Matthews coefficient: 3.66
Solvent content (%): 66.38
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: 2022-11-02
Novel Spiro[3H-indole-3,2 -pyrrolidin]-2(1H)-one Inhibitors of the MDM2-p53 Interaction: HDM2 (MDM2) IN COMPLEX WITH COMPOUND BI-0252 (PDB entry 5LAZ)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 94 residues
Sequence: QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.1809
R free: 0.2049
Average B factor: 16.249
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 293
Crystal growth procedure: RESERVOIR SOLUTION : NULL
Matthews coefficient: 2.25
Solvent content (%): 45.37
Ligand: 4-[(2~{R},3~{a}~{S},5~{S},6~{S},6~{a}~{S})-6'-chloranyl-6-(3-chloranyl-2-fluoranyl-phenyl)-4-(cyclopropylmethyl)-2'-oxidanylidene-spiro[1,2,3,3~{a},6,6~{a}-hexahydropyrrolo[3,2-b]pyrrole-5,3'-1~{H}-indole]-2-yl]benzoic acid (6ST)
Ligand formula: C30 H26 Cl2 F N3 O3
Ligand molecular weight: 566.45
Ligand SMILES: c1cc(c(c(c1)Cl)F)C2C3C(CC(N3)c4ccc(cc4)C(=O)O)N(C25c6ccc(cc6NC5=O)Cl)CC7CC7
Ligand InChI: InChI=1S/C30H26Cl2FN3O3/c31-18-10-11-20-23(12-18)35-29(39)30(20)25(19-2-1-3-21(32)26(19)33)27-24(36(30)14-15-4-5-15)13-22(34-27)16-6-8-17(9-7-16)28(37)38/h1-3,6-12,15,22,24-25,27,34H,4-5,13-14H2,(H,35,39)(H,37,38)/t22-,24+,25+,27-,30-/m1/s1
Release date: 2016-11-02
CRYSTAL STRUCTURE OF HUMAN INDOLEAMINE 2,3-DIOXYGENASE 1 (IDO1) free enzyme in the ferrous state (PDB entry 6E45)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 405 residues
Sequence: MGSSHHHHHHSSGSAAYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSAALELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1886
R free: 0.2258
Average B factor: 33.5063
Crystallization method: EVAPORATION
Crystallization pH: 6.2
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M phosphate (pH 6.2), and 15% (w/v) PEG3350
Matthews coefficient: 2.5
Solvent content (%): 50.84
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: 2018-11-14
Complex of XLF and heterodimer Ku bound to DNA (PDB entry 6ERH)
Macromolecule: X-ray repair cross-complementing protein 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4
Sequence length: 544 residues
Sequence: MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRK
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.225
R free: 0.252
Average B factor: 87.61
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 18% PEG 3350, 150 mM sodium sulfate, and 100 mM Bis-Tris-Propane
Matthews coefficient: 2.89
Solvent content (%): 57.5
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: 2018-10-17
Crystal structure of ferrous form of the crosslinked human cysteine dioxygenase (PDB entry 6BGM)
Macromolecule: Cysteine dioxygenase type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.20
Sequence length: 200 residues
Sequence: SEQTEVLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKETLFAWPDKKSNEMVKKSERVLRENQCAYINDSVGLHRVENISHTEPAVSLHLYSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTPNATSGSLENN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.206
R work: 0.1793
R free: 0.216
Average B factor: 46.7922
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M MES, 2 M ammonium sulfate, 2% PEG400
Matthews coefficient: 3.74
Solvent content (%): 67.12
Ligand: FE (II) ION (FE2)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+2]
Ligand InChI: InChI=1S/Fe/q+2
Release date: 2017-11-22
Discovery of SARxxxx92, a pan-PIM kinase inhibitor, efficacious in a KG1 tumor model (PDB entry 6VRV)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 274 residues
Sequence: PLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.1723
R free: 0.1966
Average B factor: 32.44
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 292
Crystal growth procedure: 100 mM imidazole, 1.4M sodium acetate pH 6.4
Matthews coefficient: 3.62
Solvent content (%): 66.02
Ligand: 4-chloro-1-{(1S)-1-[(3S)-3-fluoropyrrolidin-3-yl]ethyl}-3-methyl-1H-pyrrolo[2,3-b]pyridine-6-carboxamide (WFY)
Ligand formula: C15 H18 Cl F N4 O
Ligand molecular weight: 324.781
Ligand SMILES: Cc1cn(c2c1c(cc(n2)C(=O)N)Cl)C(C)C3(CCNC3)F
Ligand InChI: InChI=1S/C15H18ClFN4O/c1-8-6-21(9(2)15(17)3-4-19-7-15)14-12(8)10(16)5-11(20-14)13(18)22/h5-6,9,19H,3-4,7H2,1-2H3,(H2,18,22)/t9-,15-/m0/s1
Release date: 2020-11-04
Human ATL1 mutant - R77A bound to GDP (PDB entry 6B9D)
Macromolecule: Atlastin-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 458 residues
Sequence: SMAKNRRDRNSWGGFSEKTYEWSSEEEEPVKKAGPVQVLIVKDDHSFELDETALNRILLSEAVRDKEVVAVSVAGAFAKGKSFLMDFMLRYMYNQESVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEIFLINKPDGKKVAVLLMDTQGTFDSQSTLRDSATVFALSTMISSIQVYNLSQNVQEDDLQHLQLFTEYGRLAMEETFLKPFQSLIFLVRDWSFPYEFSYGADGGAKFLEKRLKVSGNQHEELQNVRKHIHSCFTNISCFLLPHPGLKVATNPNFDGKLKEIDDEFIKNLKILIPWLLSPESLDIKEINGNKITCRGLVEYFKAYIKIYQGEELPHPKSMLQATAEANNLAAVATAKDTYNKKMEEICGGDKPFLAPNDLQTKHLQLKEESVKLFRGVKKMGGEEFSRRYLQQLESEIDELYIQYIKHNDSKNIFHAARAAALEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2045
R free: 0.2387
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.2 M sodium malonate pH 6, 20% PEG3350, 1 mM GDP, 2 mM MgCl2
Matthews coefficient: 2.27
Solvent content (%): 45.83
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: 2017-12-06
Structure of DDR1 receptor tyrosine kinase in complex with D2099 inhibitor at 2.25 Angstroms resolution. (PDB entry 5FDP)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 337 residues
Sequence: MGHHHHHHSSGVDLGTENLYFQSMPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDGQAAQGPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1865
R free: 0.2685
Average B factor: 22.33
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293.15
Crystal growth procedure: 20% Polyethylene glycol 3350, 10% ethylene glycol, 0.1M Bis-tris propane pH 6.5, 0.2M Sodium Acetate
Matthews coefficient: 2.26
Solvent content (%): 45.63
Ligand: (4~{S})-4-methyl-~{N}-[3-[(4-methylpiperazin-1-yl)methyl]-5-(trifluoromethyl)phenyl]-2-pyrimidin-5-yl-3,4-dihydro-1~{H}-isoquinoline-7-carboxamide (5WR)
Ligand formula: C28 H31 F3 N6 O
Ligand molecular weight: 524.581
Ligand SMILES: CC1CN(Cc2c1ccc(c2)C(=O)Nc3cc(cc(c3)C(F)(F)F)CN4CCN(CC4)C)c5cncnc5
Ligand InChI: InChI=1S/C28H31F3N6O/c1-19-15-37(25-13-32-18-33-14-25)17-22-11-21(3-4-26(19)22)27(38)34-24-10-20(9-23(12-24)28(29,30)31)16-36-7-5-35(2)6-8-36/h3-4,9-14,18-19H,5-8,15-17H2,1-2H3,(H,34,38)/t19-/m1/s1
Release date: 2016-06-08
RENIN IN COMPLEXED WITH (3S,4S)-4-({[4-methoxy-3-(3-methoxypropoxy)benzoyl](propan-2-yl)amino}methyl)pyrrolidin-3-yl benzylcarbamate INHIBITOR (PDB entry 4RZ1)
Macromolecule: Renin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.15
Sequence length: 340 residues
Sequence: LTLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.199
R free: 0.2271
Average B factor: 56.94
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4
Crystallization temperature (K): 293
Crystal growth procedure: REMARK: HANGING DROP, VAPOR DIFFUSION, 1 UL PROTEIN + 1 UL RESERVOIR; PROTEIN SOLUTION: 9.4 MG/ML RENIN, 12.5 MM TRIS PH 8, 25 MM NACL; RESERVOIR SOLUTION: 21% PEG4000, 50 MM NACITRATE PH 4.0, 400 MM NACL; SOAKING: DROP PLUS 2.5 UL RESERVOIR SOLUTION PLUS 10 MM compound AND 10% DMSO FOR 20 MIN; CRYO: SOAKING SOLUTION PLUS 15% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 3.15
Solvent content (%): 61
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: 2015-03-25
BACE-1 in complex with compound #17 (PDB entry 6UVV)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 442 residues
Sequence: MAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1411
R free: 0.1862
Average B factor: 19.656
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 100mM Sodium Cacodylate pH 7.4, 12% PEG 8K, 200mM Ammonium Sulfate
Matthews coefficient: 2.6
Solvent content (%): 52.64
Ligand: (1R,2R)-2-[(4aS,7aR)-2-amino-4a,5-dihydro-4H-furo[3,4-d][1,3]thiazin-7a(7H)-yl]-N-butylcyclopropane-1-carboxamide (QJV)
Ligand formula: C14 H23 N3 O2 S
Ligand molecular weight: 297.416
Ligand SMILES: CCCCNC(=O)C1CC1C23COCC2CSC(=N3)N
Ligand InChI: InChI=1S/C14H23N3O2S/c1-2-3-4-16-12(18)10-5-11(10)14-8-19-6-9(14)7-20-13(15)17-14/h9-11H,2-8H2,1H3,(H2,15,17)(H,16,18)/t9-,10+,11+,14-/m0/s1
Release date: 2019-12-11
Crystal structure of the protein kinase CK2 catalytic subunit in complex with pyrazolo-pyrimidine macrocyclic ligand (PDB entry 5N1V)
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: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.1868
R free: 0.2293
Average B factor: 57.55
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: unknown
Matthews coefficient: 3.19
Solvent content (%): 61.39
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: 2017-05-17
HUMAN PRMT5:MEP50 Crystal Structure With MTA and Fragment Bound (PDB entry 7ZVL)
Macromolecule: Protein arginine N-methyltransferase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.320
Sequence length: 645 residues
Sequence: MDYKDDDDKAAMAVGGAGGSRVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.39
R work: 0.2158
R free: 0.286
Average B factor: 65.392
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 16% PEG3350, 100 mM Na citrate pH 5.4, 100mM Carboxylic acids
Matthews coefficient: 2.78
Solvent content (%): 55.79
Ligand: 5'-DEOXY-5'-METHYLTHIOADENOSINE (MTA)
Ligand formula: C11 H15 N5 O3 S
Ligand molecular weight: 297.334
Ligand SMILES: CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
Release date: 2022-10-19
Crystal structure of the human METTL3-METTL14 complex bound to Compound 2 (ASI_M3M_140) (PDB entry 6TTT)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 580 residues
Sequence: MSDTWSSIQAHKKQLDSLRERLQRRRKQDSGHLDLRNPEAALSPTFRSDSPVPTAPTSGGPKPSTASAVPELATDPELEKKLLHHLSDLALTLPTDAVSICLAISTPDAPATQDGVESLLQKFAAQELIEVKRGLLQDDAHPTLVTYADHSKLSAMMGAVAEKKGPGEVAGTVTGQKRRAEQDSTTVAAFASSLVSGLNSSASEPAKEPAKKSRKHAASDVDLEIESLLNQQSTKEQQSKKVSQEILELLNTTTAKEQSIVEKFRSRGRAQVQEFCDYGTKEECMKASDADRPCRKLHFRRIINKHTDESLGDCSFLNTCFHMDTCKYVHYEIDACMDSEAPGSKDHTPSQELALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1902
R free: 0.2394
Average B factor: 49.72
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 25% PEG 3350, 200 mM Magnesium acetate
Ligand: (2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-~{N}-methyl-3,4-bis(oxidanyl)oxolane-2-carboxamide (NWQ)
Ligand formula: C11 H14 N6 O4
Ligand molecular weight: 294.267
Ligand SMILES: CNC(=O)C1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C11H14N6O4/c1-13-10(20)7-5(18)6(19)11(21-7)17-3-16-4-8(12)14-2-15-9(4)17/h2-3,5-7,11,18-19H,1H3,(H,13,20)(H2,12,14,15)/t5-,6+,7-,11+/m0/s1
Release date: 2020-03-04