satarupa22/MacromolecularLigandDB huggingface dataset:
Post-catalytic Complex of Human DNA Polymerase Mu with Templating Adenine and Mn-8oxodGMP (PDB entry 6IPD)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.18684
R free: 0.21773
Average B factor: 17.671
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES pH 7.5, 18% PEG 4000
Matthews coefficient: 2.47
Solvent content (%): 50.13
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2019-05-29
Crystal Structure of human phosphodiesterase 10 in complex with 4-bromo-2,5-dimethyl-N-(2-phenylimidazo[1,2-a]pyrimidin-7-yl)pyrazole-3-carboxamide (PDB entry 5SJY)
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): 2.2
R work: 0.2018
R free: 0.2647
Average B factor: 47.554
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: 2.67
Solvent content (%): 53.87
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
Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 with compound 8a (PDB entry 8TJC)
Macromolecule: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.149
Sequence length: 397 residues
Sequence: MSVGRRRIKLLGILMMANVFIYFIMEVSKSSSQEKNGKGEVIIPKEKFWKISTPPEAYWNREQEKLNRQYNPILSMLTNQTGEAGRLSNISHLNYCEPDLRVTSVVTGFNNLPDRFKDFLLYLRCRNYSLLIDQPDKCAKKPFLLLAIKSLTPHFARRQAIRESWGQESNAGNQTVVRVFLLGQTPPEDNHPDLSDMLKFESEKHQDILMWNYRDTFFNLSLKEVLFLRWVSTSCPDTEFVFKGDDDVFVNTHHILNYLNSLSKTKAKDLFIGDVIHNAGPHRDKKLKYYIPEVVYSGLYPPYAGGGGFLYSGHLALRLYHITDQVHLYPIDDVYTGMCLQKLGLVPEKHKGFRTFDIEEKNKNNICSYVDLMLVHSRKPQEMIDIWSQLQSAHLKC
Oligomeric state: Homo 4-mer
Stoichiometry: A4
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2271
R free: 0.2753
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris 8.8, 0.16 M Sodium acetate, 25% PEG4000,  15% glycerol
Matthews coefficient: 2.33
Solvent content (%): 47.31
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2023-12-06
Crystal structure of human JMJD2A in complex with compound 14a (PDB entry 4URA)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 360 residues
Sequence: SMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.2067
R free: 0.259
Crystallization pH: 5.9
Crystal growth procedure: 0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350
Matthews coefficient: 2.71
Solvent content (%): 54.24
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2015-06-17
Crystal structure of 1-hydroxy-6-methylpyridine-2(1H)-thione bound to human carbonic anhydrase II (PDB entry 4Q7W)
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): 1.45
R work: 0.1789
R free: 0.21088
Average B factor: 12.475
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium Sulfate, pH 8.0, VAPOR DIFFUSION, temperature 291K
Matthews coefficient: 2.08
Solvent content (%): 40.99
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: 2015-03-11
Crystal structure of Aurora-A kinase in complex with an allosterically binding fragment (PDB entry 5OS2)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 265 residues
Sequence: QWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.2111
R free: 0.2509
Average B factor: 39.3632
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Tris, pH 8.5: 0.5 M NaCl: 0.2 M MgCl2: 32.5 % v/v PEG 3350
Matthews coefficient: 2.78
Solvent content (%): 55.78
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2017-11-01
Crystal structure of human KDM4D in complex with 2-1H-pyrazol-4-yloxy- 3H,4H-pyrido-3,4-d-pyrimidin-4-one (PDB entry 5FPB)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 334 residues
Sequence: GHMAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.16035
R free: 0.20319
Average B factor: 25.725
Crystallization pH: 7.4
Crystal growth procedure: 0.1M HEPES PH 7.4, 2.45M AMMONIUM SULPHATE
Matthews coefficient: 2.48
Solvent content (%): 50.37
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: 2016-01-27
The crystal structure of upain-1-W3A in complex with inactive uPA (uPA-S195A) at pH7.4 (PDB entry 4ZKS)
Macromolecule: Urokinase-type plasminogen activator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 247 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDAGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.19599
R free: 0.24457
Average B factor: 31.097
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 298
Crystal growth procedure: 50 mM sodium citrate pH 4.6, 2.0 M ammonium sulfate supplemented with 5% PEG400
Matthews coefficient: 2.07
Solvent content (%): 40.7
Release date: 2016-05-18
DNA Polymerase Mu, 8-oxodGTP:At Reaction State Ternary Complex, 50 mM Mg2+ (60min) (PDB entry 7KT7)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.1614
R free: 0.1865
Average B factor: 25.4768
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.49
Solvent content (%): 50.67
Ligand: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (8DG)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(27-5)2-26-31(22,23)29-32(24,25)28-30(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
Release date: 2021-12-15
Crystal structure of the binding domain from botulinum neurotoxin A2 bound to extracellular domain of human receptor SV2C (PDB entry 6ES1)
Macromolecule: Botulinum neurotoxin type A
Type: Protein, polypeptide(L)
Source organism: Clostridium botulinum
EC number: 3.4.24.69
Sequence length: 445 residues
Sequence: MGSSHHHHHHSSGENLYFQGHMVNTSILSIVYKKDDLIDLSRYGAKINIGDRVYYDSIDKNQIKLINLESSTIEVILKNAIVYNSMYENFSTSFWIKIPKYFSKINLNNEYTIINCIENNSGWKVSLNYGEIIWTLQDNKQNIQRVVFKYSQMVNISDYINRWIFVTITNNRLTKSKIYINGRLIDQKPISNLGNIHASNKIMFKLDGCRDPRRYIMIKYFNLFDKELNEKEIKDLYDSQSNSGILKDFWGNYLQYDKPYYMLNLFDPNKYVDVNNIGIRGYMYLKGPRGSVVTTNIYLNSTLYEGTKFIIKKYASGNEDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKDDQGIRNKCKMNLQDNNGNDIGFIGFHLYDNIAKLVASNWYNRQVGKASRTFGCSWEFIPVDDGWGESSL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.18139
R free: 0.22967
Average B factor: 27.539
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 0.160 mM HcA2 (8.27 mg/mL), 0.160 mM SV2CL4 (2.24 mg/mL), 2 mM Sialylated Thomsen-Friedenreich carbohydrate antigen (Sialyl-T). Reservoir solution: 200 mM CaCl2, 100 mM MES pH 6.0, 20 % PEG 6000
Matthews coefficient: 2.24
Solvent content (%): 45
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: 2018-04-25
EGFR (L858R, T790M, V948R) in complex with N-[3-({2-[(1-methyl-1H-pyrazol-4-yl)amino]-7H-pyrrolo[2,3-d]pyrimidin-4-yl}oxy)phenyl]prop-2-enamide (PDB entry 5HG8)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 329 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.42
R work: 0.208
R free: 0.213
Average B factor: 21.2
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 286
Crystal growth procedure: 0.1 M (5.0 uL of stock 1.0 M) HEPES (pH 7.50), 0.2 M (2.8571428571 uL of stock 3.5 M) Ammonium sulfate, 20.0 %w/v (20.0 uL of stock 50.0 %w/v) PEG 8000, 10.0 %v/v (5.0 uL of stock 100.0 %v/v) iso-propanol
Matthews coefficient: 2.05
Solvent content (%): 39.97
Ligand: N-[3-({2-[(1-methyl-1H-pyrazol-4-yl)amino]-7H-pyrrolo[2,3-d]pyrimidin-4-yl}oxy)phenyl]propanamide (634)
Ligand formula: C19 H19 N7 O2
Ligand molecular weight: 377.4
Ligand SMILES: CCC(=O)Nc1cccc(c1)Oc2c3cc[nH]c3nc(n2)Nc4cnn(c4)C
Ligand InChI: InChI=1S/C19H19N7O2/c1-3-16(27)22-12-5-4-6-14(9-12)28-18-15-7-8-20-17(15)24-19(25-18)23-13-10-21-26(2)11-13/h4-11H,3H2,1-2H3,(H,22,27)(H2,20,23,24,25)
Release date: 2016-02-03
Structure of human Leukotriene A4 hydrolase in complex with inhibitor dimethyl(2- (4-phenoxyphenoxy)ethyl)amine (PDB entry 5AEN)
Macromolecule: LEUKOTRIENE A-4 HYDROLASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 608 residues
Sequence: IVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPDVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.864
R work: 0.1704
R free: 0.1888
Average B factor: 14.8
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystal growth procedure: 1 MICROLITTER OF PROTEIN SOLUTION CONTAINING 10MM TRIS-HCL, 25MM KCL, AND 4 MG/ML TO 8 MG/ML LTA4H (PH 8) WAS MIXED AT DIFFERENT RATIOS (0.5:1, 1:1, AND 1:2) WITH PRECIPITATE SOLUTION CONTAINING 0:15M IMIDAZOLE, 0:1M SODIUM ACETATE PH 6, 14% PEG-8000, AND 5MM YBCL3, AND CRYSTALLIZED AT 17:4 C FOR TWO WEEKS BY HANGING DROP VAPOR-DIFFUSION METHOD
Matthews coefficient: 2.32
Solvent content (%): 47
Ligand: N,N-dimethyl-2-(4-phenoxyphenoxy)ethanamine (DP8)
Ligand formula: C16 H19 N O2
Ligand molecular weight: 257.328
Ligand SMILES: CN(C)CCOc1ccc(cc1)Oc2ccccc2
Ligand InChI: InChI=1S/C16H19NO2/c1-17(2)12-13-18-14-8-10-16(11-9-14)19-15-6-4-3-5-7-15/h3-11H,12-13H2,1-2H3
Release date: 2015-02-11
Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102153 (PDB entry 5QIP)
Macromolecule: Ubiquitin thioesterase OTUB2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 225 residues
Sequence: FNLISEKCDILSILRDHPENRIYRRKIEELSKRFTAIRKTKGDRNCFYRALGYSYLESLLGKSREIFKFKERVLQTPNDLLAAGFEEHKFRNFFNAFYSVVELVEKDGSVSSLLKVFNDQSASDHIVQFLRLLTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITALSQALSIALQVEYVDEMDTALNHHVFPEAATPSVYLLYKTSHYNILYA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1756
R free: 0.2043
Average B factor: 24.076
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG4K, 0.1M HEPES pH 7.0, 8% 2-propanol, 5 mM DTT
Matthews coefficient: 2.35
Solvent content (%): 47.7
Ligand: benzyl acetylcarbamate (J51)
Ligand formula: C10 H11 N O3
Ligand molecular weight: 193.199
Ligand SMILES: CC(=O)NC(=O)OCc1ccccc1
Ligand InChI: InChI=1S/C10H11NO3/c1-8(12)11-10(13)14-7-9-5-3-2-4-6-9/h2-6H,7H2,1H3,(H,11,12,13)
Release date: 2019-12-18
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z168883358 (PDB entry 5RYG)
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): 1.47
R work: 0.1746
R free: 0.2048
Average B factor: 18.61
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: 2.08
Solvent content (%): 40.94
Ligand: 1-(1,4-diazepan-1-yl)ethan-1-one (WO7)
Ligand formula: C7 H14 N2 O
Ligand molecular weight: 142.199
Ligand SMILES: CC(=O)N1CCCNCC1
Ligand InChI: InChI=1S/C7H14N2O/c1-7(10)9-5-2-3-8-4-6-9/h8H,2-6H2,1H3
Release date: 2020-11-11
Crystal structure of human Pim-1 kinase in complex with an imidazopyridazine inhibitor. (PDB entry 5KZI)
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): 2.1
R work: 0.17813
R free: 0.20469
Average B factor: 39.058
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 1.0M LiCl, 0.1M TRIS pH8.0, 20% PEG6K
Matthews coefficient: 3.27
Solvent content (%): 62.37
Ligand: ~{N}-[4-[(3~{S})-3-azanylpiperidin-1-yl]pyridin-3-yl]-2-[2,6-bis(fluoranyl)phenyl]imidazo[1,5-b]pyridazin-7-amine (6YN)
Ligand formula: C22 H21 F2 N7
Ligand molecular weight: 421.446
Ligand SMILES: c1cc(c(c(c1)F)c2ccc3cnc(n3n2)Nc4cnccc4N5CCCC(C5)N)F
Ligand InChI: InChI=1S/C22H21F2N7/c23-16-4-1-5-17(24)21(16)18-7-6-15-11-27-22(31(15)29-18)28-19-12-26-9-8-20(19)30-10-2-3-14(25)13-30/h1,4-9,11-12,14H,2-3,10,13,25H2,(H,27,28)/t14-/m0/s1
Release date: 2016-11-09
Human FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfonimidoyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-2-one (PDB entry 8CHK)
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): 1.55
R work: 0.1967
R free: 0.2328
Average B factor: 18.287
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.32M Na-K tartrate, 0.2 M ammonium citrate, 0.1M MES pH 6.5
Matthews coefficient: 2.11
Solvent content (%): 41.7
Ligand: (1S,5S,6R)-10-[[3,5-bis(chloranyl)phenyl]sulfonimidoyl]-5-ethenyl-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one (UUI)
Ligand formula: C22 H24 Cl2 N4 O2 S
Ligand molecular weight: 479.423
Ligand SMILES: C=CC1CN(C(=O)C2CCCC1N2S(=N)(=O)c3cc(cc(c3)Cl)Cl)Cc4ccccn4
Ligand InChI: InChI=1S/C22H24Cl2N4O2S/c1-2-15-13-27(14-18-6-3-4-9-26-18)22(29)21-8-5-7-20(15)28(21)31(25,30)19-11-16(23)10-17(24)12-19/h2-4,6,9-12,15,20-21,25H,1,5,7-8,13-14H2/t15-,20+,21-,31-/m0/s1
Release date: 2023-09-06
Crystal structure of EloBC-VHL-CDO1 complex bound to compound 8 molecular glue (PDB entry 8VL9)
Macromolecule: Elongin-C
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 96 residues
Sequence: MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.184
R free: 0.216
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 0.2M SODIUM CITRATE, 0.1M BIS-TRIS-PROPANE PH 6.5, 20% PEG3350
Matthews coefficient: 4.09
Solvent content (%): 69.96
Ligand: N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen-1-yl]methyl}-L-prolinamide (A1ACI)
Ligand formula: C27 H33 N5 O4
Ligand molecular weight: 491.582
Ligand SMILES: CC(=O)NC(C(=O)N1CC(CC1C(=O)NCc2ccc(c3c2cccc3)c4cc[nH]n4)O)C(C)(C)C
Ligand InChI: InChI=1S/C27H33N5O4/c1-16(33)30-24(27(2,3)4)26(36)32-15-18(34)13-23(32)25(35)28-14-17-9-10-21(22-11-12-29-31-22)20-8-6-5-7-19(17)20/h5-12,18,23-24,34H,13-15H2,1-4H3,(H,28,35)(H,29,31)(H,30,33)/t18-,23+,24-/m1/s1
Release date: 2024-03-13
Specific covalent inhibitor(18) of ERK2 (PDB entry 8AOH)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1699
R free: 0.2137
Average B factor: 21.721
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.25M (NH4)2SO4
33% MPEG 2000
0.02M Mercaptoethanol
0.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.28
Solvent content (%): 46.09
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: 2022-09-28