satarupa22/MacromolecularLigandDB huggingface dataset:
Transglutaminase 2 mutant G224V in complex with GTP (PDB entry 6A8P)
Macromolecule: Protein-glutamine gamma-glutamyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.13
Sequence length: 695 residues
Sequence: MAEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYEASVDSLTFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFEDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVVSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAHDQNSNLLIEYFRNEFGEIQGDKSEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTPQEKSEGTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQQDDGSVHKSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRANHLNKLAEKEETGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLNLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLLPLHMGLHKLVVNFESDKLKAVKGFRNVIIGPALEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.537
R work: 0.236
R free: 0.2575
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 293
Crystal growth procedure: 20 mM Mes (pH 6.8), 200 mM sodium chloride, 20 mM MgCl2, 6% PEG 3350, 5 mM DTT, 24% glycerol
Matthews coefficient: 2.54
Solvent content (%): 51.57
Ligand: GUANOSINE-5'-TRIPHOSPHATE (GTP)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2018-09-26
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z1259335913 (PDB entry 5RWY)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.1747
R free: 0.201
Average B factor: 17.81
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.1
Solvent content (%): 41.4
Ligand: 1-{1-[(2-methyl-1,3-thiazol-4-yl)methyl]piperidin-4-yl}methanamine (RWV)
Ligand formula: C11 H19 N3 S
Ligand molecular weight: 225.354
Ligand SMILES: Cc1nc(cs1)CN2CCC(CC2)CN
Ligand InChI: InChI=1S/C11H19N3S/c1-9-13-11(8-15-9)7-14-4-2-10(6-12)3-5-14/h8,10H,2-7,12H2,1H3
Release date: 2020-11-11
FACTOR INHIBITING HIF-1 ALPHA in complex with (5-(1-(3-(4-chlorophenyl)propyl)-1H-1,2,3-triazol-4-yl)-3-hydroxypicolinoyl)glycine (PDB entry 8IHZ)
Macromolecule: Hypoxia-inducible factor 1-alpha inhibitor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.30
Sequence length: 349 residues
Sequence: MAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.2267
R free: 0.2613
Average B factor: 96.82
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 1.6 M AMMONIUM SULPHATE, 6% PEG 400, 0.1 M HEPES
Matthews coefficient: 3.42
Solvent content (%): 64.05
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2024-02-28
The crystal structure of mupain-1-17 in complex with murinised human uPA at pH4.6 (PDB entry 4X1P)
Macromolecule: Urokinase-type plasminogen activator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 247 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAYHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.18051
R free: 0.21149
Average B factor: 23.192
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 298
Crystal growth procedure: 2.0M ammonium sulfate, 50mM sodium citrate pH 4.6, 5% PEG400
Matthews coefficient: 2.1
Solvent content (%): 41.36
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: 2015-10-21
Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A (PDB entry 6BGP)
Macromolecule: Calpain-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.54
Sequence length: 382 residues
Sequence: IISRNFPIIGVKEKTFEQLHKKCLEKKVLYVDPEFPPDETSLFYSQKFPIQFVWKRPPEICENPRFIIDGANRTDICQGELGDAWFLAAIACLTLNQHLLFRVIPHDQSFIENYAGIFHFQFWRYGEWVDVVIDDCLPTYNNQLVFTKSNHRNEFWSALLEKAYAKLHGSYEALKGGNTTEAMEDFTGGVAEFFEIRDAPSDMYKIMKKAIERGSLMGCSIDDGTNMTYGTSPSGLNMGELIARMVRNMDNSLLQDSDLDPRGSDERPTRTIIPVQYETRMACGLVRGHAYSVTGLDEVPFKGEKVKLVRLRNPWGQVEWNGSWSDRWKDWSFVDKDEKARLQHQVTEDGEFWMSYEDFIYHFTKLEICNLTADLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2092
R free: 0.2584
Average B factor: 68.376
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295.15
Crystal growth procedure: PEG 8000, MES, calcium chloride
Matthews coefficient: 2.03
Solvent content (%): 39.28
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2018-02-07
Human Erk2 with an Erk1/2 inhibitor (PDB entry 5NGU)
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): 2.74
R work: 0.267
R free: 0.262
Average B factor: 53.34
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 30% PegMME2K, 100mM HEPES pH 7.6, 200mM Ammonium sulfate
Matthews coefficient: 2.25
Solvent content (%): 45.4
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: 2017-04-19
Crystal structure of hMTH1 N33A in complex with TH scaffold 1 in the absence of acetate (PDB entry 6GLN)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 182 residues
Sequence: MKHHHHHHPMSDYDIPTTENLYFQGAMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWAGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.401
R work: 0.1833
R free: 0.2158
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: crystallized in: 23-27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5

soaked in: 0.27 M ammonium sulfate, 17% glycerol, 27% PEG4000, 50 mM compound
Matthews coefficient: 1.71
Solvent content (%): 28.01
Ligand: 4-phenylpyrimidin-2-amine (F3E)
Ligand formula: C10 H9 N3
Ligand molecular weight: 171.199
Ligand SMILES: c1ccc(cc1)c2ccnc(n2)N
Ligand InChI: InChI=1S/C10H9N3/c11-10-12-7-6-9(13-10)8-4-2-1-3-5-8/h1-7H,(H2,11,12,13)
Release date: 2019-02-20
hALK in complex with ((1S,2S)-1-(2,4-difluorophenyl)-2-(2-(3-methyl-1H-pyrazol-5-yl)-4-(trifluoromethyl)phenoxy)cyclopropyl)methanamine (PDB entry 7JY4)
Macromolecule: ALK tyrosine kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 322 residues
Sequence: GAMGSTDYNPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.42
R work: 0.2191
R free: 0.2554
Average B factor: 62.31
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 18.25% PEG 3350, 2% Tacsimate pH 7.0, 0.09M Tris Cl, 0.01M Tris_base
Matthews coefficient: 2.1
Solvent content (%): 41.38
Ligand: 1-{(1S,2S)-1-(2,4-difluorophenyl)-2-[2-(3-methyl-1H-pyrazol-5-yl)-4-(trifluoromethyl)phenoxy]cyclopropyl}methanamine (W47)
Ligand formula: C21 H18 F5 N3 O
Ligand molecular weight: 423.379
Ligand SMILES: Cc1cc([nH]n1)c2cc(ccc2OC3CC3(CN)c4ccc(cc4F)F)C(F)(F)F
Ligand InChI: InChI=1S/C21H18F5N3O/c1-11-6-17(29-28-11)14-7-12(21(24,25)26)2-5-18(14)30-19-9-20(19,10-27)15-4-3-13(22)8-16(15)23/h2-8,19H,9-10,27H2,1H3,(H,28,29)/t19-,20+/m0/s1
Release date: 2021-01-20
DNA Polymerase Lambda, TTP:At Mg2+ Reaction State Ternary Complex, 90 sec (PDB entry 7M44)
Macromolecule: DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 7 residues
Sequence: CAGTACT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.901
R work: 0.1949
R free: 0.2264
Average B factor: 42.93
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.82
Solvent content (%): 56.43
Ligand: THYMIDINE-5'-TRIPHOSPHATE (TTP)
Ligand formula: C10 H17 N2 O14 P3
Ligand molecular weight: 482.168
Ligand SMILES: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
Release date: 2022-07-06
Discovery and Optimisation of Potent, Efficacious and Selective Inhibitors Targeting EGFR Exon20 Insertion Mutations. Compound 16 bound to EGFR (PDB entry 8PNZ)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 329 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.2259
R free: 0.2845
Average B factor: 79.97
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.68M Na3Cit pHed to pH 7.5 using conc HCl
Matthews coefficient: 3.32
Solvent content (%): 62.97
Ligand: 1-[(3~{S})-3-[4-(6,7-dimethoxyquinazolin-4-yl)-3-(3-methoxyphenyl)pyrazol-1-yl]pyrrolidin-1-yl]propan-1-one (2I0)
Ligand formula: C27 H29 N5 O4
Ligand molecular weight: 487.55
Ligand SMILES: CCC(=O)N1CCC(C1)n2cc(c(n2)c3cccc(c3)OC)c4c5cc(c(cc5ncn4)OC)OC
Ligand InChI: InChI=1S/C27H29N5O4/c1-5-25(33)31-10-9-18(14-31)32-15-21(26(30-32)17-7-6-8-19(11-17)34-2)27-20-12-23(35-3)24(36-4)13-22(20)28-16-29-27/h6-8,11-13,15-16,18H,5,9-10,14H2,1-4H3/t18-/m0/s1
Release date: 2024-06-05
Carbonic Anhydrase IX mimic complexed with benzene sulfonamide MB10-580B (PDB entry 6OUM)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.559
R work: 0.2533
R free: 0.3035
Average B factor: 17.5746
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M sodium citrate, 50mM Tris HCl, pH 7.8
Matthews coefficient: 2.09
Solvent content (%): 41.28
Ligand: (2Z)-2-(hydroxyimino)-2,3-dihydro-1,3-benzoxazole-5-sulfonamide (N7J)
Ligand formula: C7 H7 N3 O4 S
Ligand molecular weight: 229.213
Ligand SMILES: c1cc2c(cc1S(=O)(=O)N)NC(=NO)O2
Ligand InChI: InChI=1S/C7H7N3O4S/c8-15(12,13)4-1-2-6-5(3-4)9-7(10-11)14-6/h1-3,11H,(H,9,10)(H2,8,12,13)
Release date: 2020-05-06
Human FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-2-one (PDB entry 8CHM)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 107 residues
Sequence: GVQVETISPGDGRTFPKRGQTVVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.12
R work: 0.13
R free: 0.1455
Average B factor: 10.321
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.1 M ammonium sulfate, 0.2 M cadmium chloride, 0.1M HEPES-NaOH pH 7.5
Matthews coefficient: 2.75
Solvent content (%): 55.26
Ligand: (1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfinyl-5-ethenyl-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one (UT6)
Ligand formula: C22 H23 Cl2 N3 O2 S
Ligand molecular weight: 464.408
Ligand SMILES: C=CC1CN(C(=O)C2CCCC1N2S(=O)c3cc(cc(c3)Cl)Cl)Cc4ccccn4
Ligand InChI: InChI=1S/C22H23Cl2N3O2S/c1-2-15-13-26(14-18-6-3-4-9-25-18)22(28)21-8-5-7-20(15)27(21)30(29)19-11-16(23)10-17(24)12-19/h2-4,6,9-12,15,20-21H,1,5,7-8,13-14H2/t15-,20+,21-,30+/m0/s1
Release date: 2023-09-06
Soluble epoxide hydrolase in complex with RK3 (PDB entry 8QN0)
Macromolecule: Bifunctional epoxide hydrolase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.10
Sequence length: 367 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASMLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDARNPPVVSKMLLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.16342
R free: 0.18698
Average B factor: 23.368
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG5000MME, 0.1M bis-tris pH 6.5
Matthews coefficient: 2.05
Solvent content (%): 39.98
Ligand: (3~{a}~{R},6~{a}~{S})-~{N}-[(2,4-dichlorophenyl)methyl]-5-(4-methylphenyl)sulfonyl-1,3,3~{a},4,6,6~{a}-hexahydropyrrolo[3,4-c]pyrrole-2-carboxamide (WJ5)
Ligand formula: C21 H23 Cl2 N3 O3 S
Ligand molecular weight: 468.397
Ligand SMILES: Cc1ccc(cc1)S(=O)(=O)N2CC3CN(CC3C2)C(=O)NCc4ccc(cc4Cl)Cl
Ligand InChI: InChI=1S/C21H23Cl2N3O3S/c1-14-2-6-19(7-3-14)30(28,29)26-12-16-10-25(11-17(16)13-26)21(27)24-9-15-4-5-18(22)8-20(15)23/h2-8,16-17H,9-13H2,1H3,(H,24,27)/t16-,17+
Release date: 2024-02-14
DNA Polymerase Beta crystallized in PEG 400 (PDB entry 5U8G)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.166
R work: 0.1793
R free: 0.2248
Average B factor: 40.6452
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 24% PEG 400, 30 mM potassium sodium tartrate, 1% 1,4-dioxane
Matthews coefficient: 2.37
Solvent content (%): 48.02
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-04-26
FGFR1 kinase domain (residues 458-765) with mutations C488A, C584S in complex with 34. (PDB entry 7OZD)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: GAGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.1995
R free: 0.2412
Average B factor: 44.319
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.7
Crystallization temperature (K): 291
Crystal growth procedure: 0.185M ammonium sulfate, 20% v/v ethylene glycol, 17% w/v PEG 8000, 0.1M PCPT
Matthews coefficient: 2.67
Solvent content (%): 53.92
Ligand: N-[6-(4-hydroxyphenyl)-1H-indazol-3-yl]benzamide (42I)
Ligand formula: C20 H15 N3 O2
Ligand molecular weight: 329.352
Ligand SMILES: c1ccc(cc1)C(=O)Nc2c3ccc(cc3[nH]n2)c4ccc(cc4)O
Ligand InChI: InChI=1S/C20H15N3O2/c24-16-9-6-13(7-10-16)15-8-11-17-18(12-15)22-23-19(17)21-20(25)14-4-2-1-3-5-14/h1-12,24H,(H2,21,22,23,25)
Release date: 2021-12-01
Kallikrein-related peptidase 10 complex with Zn2+ (PDB entry 5LPE)
Macromolecule: Kallikrein-10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 234 residues
Sequence: LDPEAYGSPCARGSQPWQVSLFNGLSFHCAGVLVDQSWVLTAAHCGNKPLWARVGDDHLLLLQGEQLRRTTRSVVHPKYHQGSGPILPRRTDEHDLMLLKLARPVVLGPRVRALQLPYRCAQPGDQCQVAGWGTTAARRVKYNKGLTCSSITILSPKECEVFYPGVVTNNMICAGLDRGQDPCQSDSGGPLVCDETLQGILSWGVYPCGSAQHPAVYTQICKYMSWINKVIRSN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2198
R free: 0.2777
Average B factor: 37.4763
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM  ammonium sulphate, 100 mM MES
Matthews coefficient: 1.93
Solvent content (%): 36.23
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: 2016-10-05
APE1 exonuclease substrate complex L104R (PDB entry 6W3Q)
Macromolecule: TCGACGGATCC
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 11 residues
Sequence: TCGACGGATCC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.49
R work: 0.2216
R free: 0.2593
Average B factor: 75.43
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Matthews coefficient: 2.73
Solvent content (%): 54.86
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2020-06-10
XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM010946a (PDB entry 5S80)
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): 1.67
R work: 0.1955
R free: 0.2305
Average B factor: 23.63
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: 2.57
Solvent content (%): 52.21
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