satarupa22/MacromolecularLigandDB huggingface dataset:
HsNMT1 in complex with both MyrCoA and Acetylated-GKSFSKPR peptide reveals N-terminal Lysine Myristoylation (PDB entry 6SK2)
Macromolecule: Apoptosis-inducing factor 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 9 residues
Sequence: XGKSFSKPR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.90000651019
R work: 0.171966781113
R free: 0.219991662291
Average B factor: 31.6244340982
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 22% PEG8K, 100mM Sodium Citrate pH 5.6, 100mM MgCl2, 100mM NaCl
Matthews coefficient: 2.16
Solvent content (%): 43.02
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: 2020-03-18
Crystal Structure of human phosphodiesterase 10 in complex with 6-cyclopropyl-N-[1-methyl-5-(methylcarbamoyl)pyrazol-4-yl]-3-(pyrimidin-5-ylamino)pyrazine-2-carboxamide (PDB entry 5SE5)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.1858
R free: 0.2259
Average B factor: 42.853
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.61
Solvent content (%): 52.87
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: 2022-10-12
Crystal structure of the human UBR-box domain from UBR2 in complex with asymmetrically double methylated arginine peptide (PDB entry 5TDB)
Macromolecule: E3 ubiquitin-protein ligase UBR2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 76 residues
Sequence: GPLGSLCGRVFKVGEPTYSCRDCAVDPTCVLCMECFLGSIHRDHRYRMTTSGGGGFCDCGDTEAWKEGPYCQKHEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.101
R work: 0.1248
R free: 0.134
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5 and 25% PEG 3350
Matthews coefficient: 1.73
Solvent content (%): 28.96
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: 2017-03-22
Identification and characterization of inhibitors covalently modifying catalytic cysteine of UBE2T and blocking ubiquitin transfer (PDB entry 8JVE)
Macromolecule: Ubiquitin-conjugating enzyme E2 T
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 156 residues
Sequence: GSMQRASRLKRELHMLATEPPPGITCWQDKDQMDDLRAQILGGANTPYEKGVFKLEVIIPERYPFEPPQIRFLTPIYHPNIDSAGRICLDVLKLPPKGAWRPSLNIATVLTSIQLLMSEPNPDDPLMADISSEFKYNKPAFLKNARQWTEKHARQK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.2168
R free: 0.2466
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 3.5 M Sodium formate pH 7.0
Matthews coefficient: 3.89
Solvent content (%): 68.4
Ligand: 1-(3-methoxyphenyl)-1,2,3,4-tetrazole (V6C)
Ligand formula: C8 H8 N4 O
Ligand molecular weight: 176.175
Ligand SMILES: COc1cccc(c1)n2cnnn2
Ligand InChI: InChI=1S/C8H8N4O/c1-13-8-4-2-3-7(5-8)12-6-9-10-11-12/h2-6H,1H3
Release date: 2023-11-29
Tankyrase 2 in complex with an inhibitor (OM-1720) (PDB entry 6TKS)
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): 2.5
R work: 0.2138
R free: 0.2592
Average B factor: 53.242
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295.15
Crystal growth procedure: 7.5-25% PEG 6000, Bicine, pH=9.0
Matthews coefficient: 2.16
Solvent content (%): 42.98
Ligand: ~{N}-[3-[5-(5-ethoxypyridin-2-yl)-4-(2-fluorophenyl)-1,2,4-triazol-3-yl]cyclobutyl]-1,6-naphthyridine-2-carboxamide (NJ2)
Ligand formula: C28 H24 F N7 O2
Ligand molecular weight: 509.534
Ligand SMILES: CCOc1ccc(nc1)c2nnc(n2c3ccccc3F)C4CC(C4)NC(=O)c5ccc6cnccc6n5
Ligand InChI: InChI=1S/C28H24FN7O2/c1-2-38-20-8-10-23(31-16-20)27-35-34-26(36(27)25-6-4-3-5-21(25)29)18-13-19(14-18)32-28(37)24-9-7-17-15-30-12-11-22(17)33-24/h3-12,15-16,18-19H,2,13-14H2,1H3,(H,32,37)/t18-,19-
Release date: 2020-07-08
Crystal structure of WNK3 kinase and CCT1 didomain in a unphosphorylated state (PDB entry 5O2C)
Macromolecule: Serine/threonine-protein kinase WNK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 380 residues
Sequence: SMEKNEKEMEEEAEMKAVATSPSGRFLKFDIELGRGAFKTVYKGLDTETWVEVAWCELQDRKLTKAEQQRFKEEAEMLKGLQHPNIVRFYDSWESILKGKKCIVLVTELMTSGTLKTYLKRFKVMKPKVLRSWCRQILKGLQFLHTRTPPIIHRDLKCDNIFITGPTGSVKIGDLGLATLMRTSFAKSVIGTPEFMAPEMYEEHYDESVDVYAFGMCMLEMATSEYPYSECQNAAQIYRKVTSGIKPASFNKVTDPEVKEIIEGCIRQNKSERLSIRDLLNHAFFAEDTGLRVELAEEDDCSNSSLALRLWVEDPKKLKGKHKDNEAIEFSFNLETDTPEEVAYEMVKSGFFHESDSKAVAKSIRDRVTPIKKTREKKPA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1851
R free: 0.2542
Average B factor: 44.3
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 18% PEG3350, 0.1 M Citrate pH 5
Matthews coefficient: 2.87
Solvent content (%): 57.15
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2017-06-28
CRYSTAL STRUCTURE OF JANUS KINASE 2 IN COMPLEX WITH N,N-DICYCLOPROPYL-7-[(DIMETHYL-1,3-THIAZOL-2-YL)AMINO]-10-ETHYL-3-METHYL-3,5,8,10-TETRAAZATRICYCLO[7.3.0.02,6] DODECA-1(9),2(6),4,7,11-PENTAENE-11-CARBOXAMIDE (PDB entry 5CF5)
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): 2.45
R work: 0.1865
R free: 0.1994
Average B factor: 49.27
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: 2.91
Solvent content (%): 57.66
Ligand: N,N-dicyclopropyl-4-[(4,5-dimethyl-1,3-thiazol-2-yl)amino]-6-ethyl-1-methyl-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridine-7-carboxamide (50W)
Ligand formula: C23 H27 N7 O S
Ligand molecular weight: 449.572
Ligand SMILES: CCn1c(cc2c1nc(c3c2n(cn3)C)Nc4nc(c(s4)C)C)C(=O)N(C5CC5)C6CC6
Ligand InChI: InChI=1S/C23H27N7OS/c1-5-29-17(22(31)30(14-6-7-14)15-8-9-15)10-16-19-18(24-11-28(19)4)20(26-21(16)29)27-23-25-12(2)13(3)32-23/h10-11,14-15H,5-9H2,1-4H3,(H,25,26,27)
Release date: 2015-08-26
Structure of Maternal embryonic leucine zipper kinase bound to LDSM276 (PDB entry 6VXR)
Macromolecule: Maternal embryonic leucine zipper kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 339 residues
Sequence: SMKDYDELLKYYELHETIGTGGFAKVKLACHILTGEMVAIKIMDKNTLGSDLPRIKTEIEALKNLRHQHICQLYHVLETANKIFMVLEYCPGGELFDYIISQDRLSEEETRVVFRQIVSAVAYVHSQGYAHRDLKPENLLFDEYHKLKLIDFGLCAKPKGNKDYHLQTCCGSLAYAAPELIQGKSYLGSEADVWSMGILLYVLMCGFLPFDDDNVMALYKKIMRGKYDVPKWLSPSSILLLQQMLQVDPKKRISMKNLLNHPWIMQDYNYPVEWQSKNPFIHLDDDCVTELSVHHRNNRQTMEDLISLWQYDHLTATYLLLLAKKARGKPVRLRLSSFS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.219
R free: 0.2483
Average B factor: 51.597
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 1,500
Matthews coefficient: 2.37
Solvent content (%): 48.2
Ligand: (7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5,8-di(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one (F7D)
Ligand formula: C19 H15 F2 N5 O2
Ligand molecular weight: 383.352
Ligand SMILES: CC1C(=O)N(c2cnc(nc2N1CC#C)Nc3cc(c(c(c3)F)O)F)CC#C
Ligand InChI: InChI=1S/C19H15F2N5O2/c1-4-6-25-11(3)18(28)26(7-5-2)15-10-22-19(24-17(15)25)23-12-8-13(20)16(27)14(21)9-12/h1-2,8-11,27H,6-7H2,3H3,(H,22,23,24)/t11-/m1/s1
Release date: 2020-07-29
Crystal Structure of small molecule alpha,beta-ketoamide 4 covalently bound to K-Ras(G12R) (PDB entry 8CX5)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGARGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.1885
R free: 0.2211
Average B factor: 24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M MES 6.5
30% w/v PEG 4K
Matthews coefficient: 2.04
Solvent content (%): 39.73
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: 2022-08-31
Crystal structure of human Pim-1 kinase in complex with an azaspiro pyrazinyl-indazole inhibitor. (PDB entry 4WRS)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 286 residues
Sequence: MAHHHHHHDEVDGPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.17891
R free: 0.20781
Average B factor: 44.684
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 1.0M LiCl, 0.1M TRIS, 20% PEG6K
Matthews coefficient: 3.37
Solvent content (%): 63.46
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: 2015-02-04
Crystal structure of a mutated catalytic domain of Human MMP12 in complex with an hydroxamate analogue of RXP470 (PDB entry 5D2B)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 159 residues
Sequence: MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1544
R free: 0.1747
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 293
Crystal growth procedure: Protein : hMMP12 F171D at 820 micro-M + 10 milli-M AHA + 0.708 milli-M inhibitor.
Precipitant : 20% PEG4000, 0.2 M TRIS pH 9.5
Cryoprotectant : 10 % diethylene glycol + 5 % glycerol + 10 % 1,2-propanediol + 5 % 1,4-dioxane + 25% PEG6000 +  0.1 M TRIS HCl pH 8.0
Matthews coefficient: 2.27
Solvent content (%): 45.81
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: 2016-08-17
JAK2 JH2 IN COMPLEX WITH JAK315 (PDB entry 7T0P)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.1945
R free: 0.2474
Average B factor: 21.2521
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M TRIS, PH 8.0 0.2M SODIUM ACETATE, 0.001 M TCEP, 12-24% PEG 4,000
Matthews coefficient: 2.29
Solvent content (%): 46.18
Ligand: 4'-{[5-amino-3-(4-sulfamoylanilino)-1H-1,2,4-triazole-1-carbonyl]amino}-4-(benzyloxy)[1,1'-biphenyl]-3-carboxylic acid (E3W)
Ligand formula: C29 H25 N7 O6 S
Ligand molecular weight: 599.617
Ligand SMILES: c1ccc(cc1)COc2ccc(cc2C(=O)O)c3ccc(cc3)NC(=O)n4c(nc(n4)Nc5ccc(cc5)S(=O)(=O)N)N
Ligand InChI: InChI=1S/C29H25N7O6S/c30-27-34-28(32-21-11-13-23(14-12-21)43(31,40)41)35-36(27)29(39)33-22-9-6-19(7-10-22)20-8-15-25(24(16-20)26(37)38)42-17-18-4-2-1-3-5-18/h1-16H,17H2,(H,33,39)(H,37,38)(H2,31,40,41)(H3,30,32,34,35)
Release date: 2022-06-15
Multiconformer model of apo WT PTP1B with glycerol at 100 K (ALTERNATIVE REFINEMENT OF PDB 1SUG showing conformational heterogeneity) (PDB entry 6B90)
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: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.158
R free: 0.1926
Average B factor: 32.3237
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: well solution: PEG 8000, magnesium acetate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 3.36
Solvent content (%): 63.34
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: 2018-06-20
Crystal structure of human carbonic anhydrase isozyme II with 2-chloro-4-{[(4-methyl-6-oxo-1,6-dihydropyrimidin-2-yl)thio]acetyl}benzenesulfonamide (PDB entry 4QSA)
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): 1.501
R work: 0.166
R free: 0.205
Average B factor: 15.163
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 2M sodium malonate pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Matthews coefficient: 2
Solvent content (%): 38
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: 2015-01-21
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with PCM-0102716 (PDB entry 5QH9)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.1835
R free: 0.2058
Average B factor: 30.06
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.16
Solvent content (%): 70.44
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2019-03-27
Crystal Structure of a UbcH5b~Ub conjugate (PDB entry 5ULF)
Macromolecule: Ubiquitin-conjugating enzyme E2 D2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 152 residues
Sequence: GPLGSMALKRIHKELNDLARDPPAQSRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSISSLLSDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2274
R free: 0.2612
Average B factor: 23.499
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 289
Crystal growth procedure: 100 mM bis-Tris pH 5.5, 150 mM ammonium sulfate, 20% PEG 3350
Matthews coefficient: 2.14
Solvent content (%): 42.55
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: 2017-06-07
Crystal structure of human 14-3-3 gamma in complex with CFTR R-domain peptide pS768-pS795 (PDB entry 5D3E)
Macromolecule: 14-3-3 protein gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 241 residues
Sequence: MGSMVDREQLVQKARLAEQAERYDDMAAAMKNVTELNEPLSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTSADGNEKKIEMVRAYREKIEKELEAVCQDVLSLLDNYLIKNCSETQYESKVFYLKMKGDYYRYLAEVATGEKRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALNYSVFYYEIQNAPEQACHLAKTAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.202
R free: 0.2436
Average B factor: 63.19
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: HEPES, NaCl, DTT, (NH4)2SO4, Poly(acrylic acid sodium salt 2100
Matthews coefficient: 3.09
Solvent content (%): 60.23
Release date: 2016-03-16
Crystal structure of FGFR1 kinase domain with Pemigatinib (PDB entry 7WCL)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 310 residues
Sequence: GPAGVSEYELPEDPRWELPRDRLVLGKPLGEGCFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.495
R work: 0.1931
R free: 0.2301
Average B factor: 44.4646
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 18% (w/v) PEG 8000, 0.2 M LiSO4, 0.1 M MES (pH 6.5)
Matthews coefficient: 2.37
Solvent content (%): 48.02
Ligand: 11-[2,6-bis(fluoranyl)-3,5-dimethoxy-phenyl]-13-ethyl-4-(morpholin-4-ylmethyl)-5,7,11,13-tetrazatricyclo[7.4.0.0^{2,6}]trideca-1(9),2(6),3,7-tetraen-12-one (8ZF)
Ligand formula: C24 H27 F2 N5 O4
Ligand molecular weight: 487.499
Ligand SMILES: CCN1c2c3cc([nH]c3ncc2CN(C1=O)c4c(c(cc(c4F)OC)OC)F)CN5CCOCC5
Ligand InChI: InChI=1S/C24H27F2N5O4/c1-4-30-21-14(11-27-23-16(21)9-15(28-23)13-29-5-7-35-8-6-29)12-31(24(30)32)22-19(25)17(33-2)10-18(34-3)20(22)26/h9-11H,4-8,12-13H2,1-3H3,(H,27,28)
Release date: 2022-09-14
PKA variant as Aurora B mimic in complex with a dianilinopyrimidine inhibitor (PDB entry 6FRX)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.11
Sequence length: 351 residues
Sequence: MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIRTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRIQQAVNFPFLVKLEFSFKDNSNLYMVLEYAPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIKVADFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.1895
R free: 0.2264
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PKA-AU6 at 10mg/ml in 25mM BisTRIS/HCl (pH7.0), 150mM KCl, 1.5mM octanoyl-N-methylglucamide and 0.8mM PKI was equilibrated against 12-26% (v/v) methanol.
Matthews coefficient: 2.56
Solvent content (%): 51.92
Ligand: ~{N}-[3-[(5-chloranyl-2-phenylazanyl-pyrimidin-4-yl)amino]phenyl]prop-2-enamide (E3Z)
Ligand formula: C19 H16 Cl N5 O
Ligand molecular weight: 365.816
Ligand SMILES: C=CC(=O)Nc1cccc(c1)Nc2c(cnc(n2)Nc3ccccc3)Cl
Ligand InChI: InChI=1S/C19H16ClN5O/c1-2-17(26)22-14-9-6-10-15(11-14)23-18-16(20)12-21-19(25-18)24-13-7-4-3-5-8-13/h2-12H,1H2,(H,22,26)(H2,21,23,24,25)
Release date: 2019-03-13