satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human DHODH in complex with inhibitor 0944 (PDB entry 6LP7)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 366 residues
Sequence: ATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.802
R work: 0.1531
R free: 0.1705
Average B factor: 25.74
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: hepes pH4.6
2M AMMONIUM SULPHATE
30%Glycerol
Matthews coefficient: 3.68
Solvent content (%): 66.56
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2020-09-30
Structure of human PARP1 catalytic domain bound to a quinazoline-2,4(1H,3H)-dione inhibitor (PDB entry 5WRY)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 352 residues
Sequence: HMKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.22805
R free: 0.27453
Average B factor: 28.112
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 2.5M AMMONIUM SULFATE, 100mM TRIS
Matthews coefficient: 2.27
Solvent content (%): 45.75
Ligand: N-[(3R)-1-(cyclopropylmethyl)pyrrolidin-3-yl]-5-[(2,4-dioxo-3,4-dihydroquinazolin-1(2H)-yl)methyl]-2-fluorobenzamide (4YR)
Ligand formula: C24 H25 F N4 O3
Ligand molecular weight: 436.479
Ligand SMILES: c1ccc2c(c1)C(=O)NC(=O)N2Cc3ccc(c(c3)C(=O)NC4CCN(C4)CC5CC5)F
Ligand InChI: InChI=1S/C24H25FN4O3/c25-20-8-7-16(13-29-21-4-2-1-3-18(21)22(30)27-24(29)32)11-19(20)23(31)26-17-9-10-28(14-17)12-15-5-6-15/h1-4,7-8,11,15,17H,5-6,9-10,12-14H2,(H,26,31)(H,27,30,32)/t17-/m1/s1
Release date: 2017-01-25
Bicycle Toxin Conjugate bound to EphA2 (PDB entry 6RW2)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 193 residues
Sequence: ASRGSHHHHHHGASDDDDKEVVLLDFAAAGGELGWLTHPYGKGWDLMQNIMNDMPIYMYSVCNVMSGDQDNWLRTNWVYRGEAERIFIELKFTVRDCNSFPGGASSCKETFNLYYAESDLDYGTNFQKRLFTKIDTIAPDEITVSSDFEARHVKLNVEERSVGPLTRKGFYLAFQDIGACVALLSVRVYYKKC
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.211
R free: 0.2646
Average B factor: 41.752
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M sodium acetate
0.2M lithium sulphate
8-10% PEG 6000
Matthews coefficient: 3.55
Solvent content (%): 65.39
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: 2020-04-08
LSD1-FCPA-MPE N5 adduct model (PDB entry 6KGR)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 669 residues
Sequence: GPLGSHMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.32
R work: 0.1682
R free: 0.1983
Average B factor: 66.02
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M HEPES (pH 7.5), 5% MPD, 3.5-4.0% PEG MME 2000
Matthews coefficient: 3.73
Solvent content (%): 67.05
Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL (MPD)
Ligand formula: C6 H14 O2
Ligand molecular weight: 118.174
Ligand SMILES: CC(CC(C)(C)O)O
Ligand InChI: InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
Release date: 2020-03-25
Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 16) (PDB entry 7KBH)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 377 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.1495
R free: 0.2207
Average B factor: 38.72
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
Matthews coefficient: 2.46
Solvent content (%): 49.93
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: 2020-12-30
Crystal structure of APOBEC3A in complex with a single-stranded DNA (PDB entry 5KEG)
Macromolecule: DNA dC->dU-editing enzyme APOBEC-3A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4
Sequence length: 203 residues
Sequence: GPGHMEASPASGPRHLMDPHIFTSNFNNGIGRHKTYLCYEVERLDNGTSVKMDQHRGFLHNQAKNLLCGFYGRHAALRFLDLVPSLQLDPAQIYRVTWFISWSPCFSWGCAGEVRAFLQENTHVRLRIFAARIYDYDPLYKEALQMLRDAGAQVSIMTYDEFKHCWDTFVDHQGAPFQPWDGLDEHSQALSGRLRAILQNQGN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.177
R free: 0.225
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MOPS
50 mM MgCl2
50 mM CaCl2
23% PEG 3350
15% 2-methyl-2,4-pentanediol
Matthews coefficient: 2.13
Solvent content (%): 42.13
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: 2017-05-10
X-ray structure of human PPAR alpha ligand binding domain-elafibranor-SRC1 coactivator peptide co-crystals obtained by soaking (PDB entry 8HUQ)
Macromolecule: Peroxisome proliferator-activated receptor alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 273 residues
Sequence: GSHMTADLKSLAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYRDMY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1864
R free: 0.2135
Average B factor: 34.4439
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris (pH 8.5), 25%(w/v) PEG3350
Matthews coefficient: 2.15
Solvent content (%): 42.91
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: 2023-08-09
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000684a (PDB entry 7GTG)
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): 1.69
R work: 0.1974
R free: 0.2326
Average B factor: 41.104
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: 3.36
Solvent content (%): 63.37
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: 2024-01-24
PDE10 complexed with6-chloro-N-[(2,4-dimethylthiazol-5-yl)methyl]-5-methyl-2-[2-(2-pyridyl)ethoxy]pyrimidin-4-amine (PDB entry 5C2E)
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: 362 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2489
R free: 0.2801
Average B factor: 49.28
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 100mM HEPES pH 7.0, 20% PEG3350, 200mM MgCl2, and 10mM 2-Mercaptoethanol
Matthews coefficient: 1.88
Solvent content (%): 34.42
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: 2015-12-02
The N4BP1 CUE-like domain in complex with linear di-Ubiquitin (PDB entry 8T48)
Macromolecule: NEDD4-binding protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 68 residues
Sequence: MHHHHHHGENLYFQGSQRSSAETSELREALLKIFPDSEQKLKIDQILAAHPYMKDLNALSALVLDGNS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1603
R free: 0.2178
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris pH 8.5, 30% (w/v) PEG 4K, 0.2 M Li2SO4
Matthews coefficient: 1.99
Solvent content (%): 38.21
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: 2024-03-13
Tubulin Glutamylase (PDB entry 4YLS)
Macromolecule: Tubulin polyglutamylase TTLL7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6
Sequence length: 487 residues
Sequence: GSFTKKKGTITANVAGTKFEIVRLVIDEMGFMKTPDEDETSNLIWCDSAVQQEKISELQNYQRINHFPGMGEICRKDFLARNMTKMIKSRPLDYTFVPRTWIFPAEYTQFQNYVKELKKKRKQKTFIVKPANGAMGHGISLIRNGDKLPSQDHLIVQEYIEKPFLMEGYKFDLRIYILVTSCDPLKIFLYHDGLVRMGTEKYIPPNESNLTQLYMHLTNYSVNKHNEHFERDETENKGSKRSIKWFTEFLQANQHDVAKFWSDISELVVKTLIVAEPHVLHAYRMCRPGQPPGSESVCFEVLGFDILLDRKLKPWLLQINRAPSFGTDQKIDYDVKRGVLLNALKLLNIRTSDKRRNLAKQKAEAQRRLYGQNSIKRLLPGSSDWEQQRHQLERRKEELKERLAQVRKQISREEHENRHMGNYRRIYPPEDKALLEKYENLLAVAFQTFLSGRAASFQRELNNPLKRMKEEDILDLLEQCEIDDEKL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.21
R free: 0.246
Average B factor: 73.26
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 279
Crystal growth procedure: PEG 8000, magnesium acetate
Matthews coefficient: 2.73
Solvent content (%): 55.02
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2015-06-17
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dCTP analogue (PDB entry 6CTV)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 16 residues
Sequence: CCGACGTCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.18
R free: 0.2202
Average B factor: 31.4264
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.27
Solvent content (%): 45.79
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2018-06-20
XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM000376d (PDB entry 5S7X)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1503
R free: 0.1691
Average B factor: 17.282
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M citrate pH 6.0, 1.4M ammonium sulfate, 0.2M sodium/potassium tartrate
Matthews coefficient: 2.58
Solvent content (%): 52.3
Ligand: 4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine (LU8)
Ligand formula: C27 H32 N2 O3
Ligand molecular weight: 432.555
Ligand SMILES: Cc1c(cncc1c2cc(c(c(c2)OC)OC)OC)c3ccc(cc3)C4CCN(CC4)C
Ligand InChI: InChI=1S/C27H32N2O3/c1-18-23(21-8-6-19(7-9-21)20-10-12-29(2)13-11-20)16-28-17-24(18)22-14-25(30-3)27(32-5)26(15-22)31-4/h6-9,14-17,20H,10-13H2,1-5H3
Release date: 2021-06-23
Crystal structure of PIM1 kinase in complex with small-molecule inhibitor (PDB entry 5O11)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 298 residues
Sequence: HHHHHHSQDPNSMKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.16461
R free: 0.21159
Average B factor: 43.251
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: Tris, potassium sodium tartrate tetrahydrate
Matthews coefficient: 3.41
Solvent content (%): 63.91
Ligand: 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid (3NG)
Ligand formula: C19 H12 Cl N3 O2
Ligand molecular weight: 349.77
Ligand SMILES: c1cc(cc(c1)Cl)Nc2c3ccncc3c4ccc(cc4n2)C(=O)O
Ligand InChI: InChI=1S/C19H12ClN3O2/c20-12-2-1-3-13(9-12)22-18-15-6-7-21-10-16(15)14-5-4-11(19(24)25)8-17(14)23-18/h1-10H,(H,22,23)(H,24,25)
Release date: 2017-11-01
FIBROBLAST GROWTH FACTOR RECEPTOR 4 KINASE DOMAIN (449-753) IN COMPLEX WITH IRREVERSIBLE LIGAND CGA159527 (PDB entry 5NWZ)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 307 residues
Sequence: GPLVSLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDRVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.37
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: TRIS, 25% PEG3350.
                      1MM EDTA, PH8.0
Matthews coefficient: 2.37
Solvent content (%): 48.12
Ligand: ~{N}-[3-[2-(3,5-dimethoxyphenyl)ethyl]-1~{H}-pyrazol-5-yl]-2-(propanoylamino)benzamide (9CT)
Ligand formula: C23 H26 N4 O4
Ligand molecular weight: 422.477
Ligand SMILES: CCC(=O)Nc1ccccc1C(=O)Nc2cc(n[nH]2)CCc3cc(cc(c3)OC)OC
Ligand InChI: InChI=1S/C23H26N4O4/c1-4-22(28)24-20-8-6-5-7-19(20)23(29)25-21-13-16(26-27-21)10-9-15-11-17(30-2)14-18(12-15)31-3/h5-8,11-14H,4,9-10H2,1-3H3,(H,24,28)(H2,25,26,27,29)
Release date: 2018-04-04
Crystal structure of human carbonic anhydrase isozyme I with 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide (PDB entry 5E2M)
Macromolecule: Carbonic anhydrase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSPDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.182
R free: 0.207
Average B factor: 21.131
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer contains 0.1M TrisHCl (pH 8.5), 0.2M ammonium acetate, 28% of PEG4000
Matthews coefficient: 2.26
Solvent content (%): 45.3
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: 2016-10-05
Structure of the nuclease subunit of human mitochondrial RNase P (MRPP3) at 1.98A (PDB entry 4XGM)
Macromolecule: Mitochondrial ribonuclease P protein 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.26.5
Sequence length: 379 residues
Sequence: SMTLEPRGYSLLIRGLIHSDRWREALLLLEDIKKVITPSKKNYNDCIQGALLHQDVNTAWNLYQELLGHDIVPMLETLKAFFDFGKDIKDDNYSNKLLDILSYLRNNQLYPGESFAHSIKTWFESVPGKQWKGQFTTVRKSGQCSGCGKTIESIQLSPEEYECLKGKIMRDVIDGGDQYRKTTPQELKRFENFIKSRPPFDVVIDGLNVAKMFPKVRESQLLLNVVSQLAKRNLRLLVLGRKHMLRRSSQWSRDEMEEVQKQASCFFADDISEDDPFLLYATLHSGNHCRFITRDLMRDHKACLPDAKTQRLFFKWQQGHQLAIVNRFPGSKLTFQRILSYDTVVQTTGDSWHIPYDEDLVERCSCEVPTKWLCLHQKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1929
R free: 0.2263
Average B factor: 63.5861
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: HEPES, PEG 6000, magnesium chloride
Matthews coefficient: 2.81
Solvent content (%): 56.27
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: 2015-05-13
Crystal structure of mandrill SAMHD1 (amino acid residues 1-114) bound to Vpx isolated from mandrill and human DCAF1 (amino acid residues 1058-1396) (PDB entry 5AJA)
Macromolecule: PROTEIN VPRBP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 361 residues
Sequence: MASFPKYGGVDGGCFDRHLIFSRFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVGRQRLAEELALVPRGSSAHHHHHHHHHH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.649
R work: 0.1735
R free: 0.227
Average B factor: 87.6
Crystal growth procedure: 0.16 M TRISODIUM CITRATE-HCL PH 5.2, 4% PEG 6000
Matthews coefficient: 3.04
Solvent content (%): 60
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: 2015-04-22
Crystal structure of the ACVR1 (ALK2) kinase in complex with a Quinazolinone based ALK2 inhibitor with a 5-methyl core. (PDB entry 6GI6)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.2132
R free: 0.2625
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 1.5M ammonium sulfate, 0.1M sodium chloride, 0.1M bis-tris pH 6.5
Matthews coefficient: 2.49
Solvent content (%): 50.67
Ligand: 5-methyl-6-quinolin-5-yl-3~{H}-quinazolin-4-one (EZB)
Ligand formula: C18 H13 N3 O
Ligand molecular weight: 287.315
Ligand SMILES: Cc1c(ccc2c1C(=O)NC=N2)c3cccc4c3cccn4
Ligand InChI: InChI=1S/C18H13N3O/c1-11-12(7-8-16-17(11)18(22)21-10-20-16)13-4-2-6-15-14(13)5-3-9-19-15/h2-10H,1H3,(H,20,21,22)
Release date: 2018-05-23