satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of MYST acetyltransferase domain in complex with N-(1-(5-bromo-2-methoxyphenyl)-1H-1,2,3-triazol-4-yl)-2-methoxybenzenesulfonamide (PDB entry 8W13)
Macromolecule: Histone acetyltransferase KAT8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 278 residues
Sequence: GSTKVKYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPPGKEIYRKSNISVHEVDGKDHKIYCQNLCLLAKLFLDHKTLYFDVEPFVFYILTEVDRQGAHIVGYFSKEKESPDGNNVSCIMILPPYQRRGYGRFLIAFSYELSKLESTVGSPEKPLSDLGKLSYRSYWSSVLLENLRDFRGTLSIKDLSQMTSITQNDIISTLQSLNMVKYWKGQHVICVTPKLVEEHLKSAQYKKPPITVDSVCLKWAPPK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.16415
R free: 0.20352
Average B factor: 27.105
Crystallization method: EVAPORATION
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M tris pH7.0,2M NaCl,0.22M MgCl2
Matthews coefficient: 2.51
Solvent content (%): 51.04
Ligand: N-[(1M)-1-(5-bromo-2-methoxyphenyl)-1H-1,2,3-triazol-4-yl]-2-methoxybenzene-1-sulfonamide (A1AEW)
Ligand formula: C16 H15 Br N4 O4 S
Ligand molecular weight: 439.284
Ligand SMILES: COc1ccccc1S(=O)(=O)Nc2cn(nn2)c3cc(ccc3OC)Br
Ligand InChI: InChI=1S/C16H15BrN4O4S/c1-24-13-8-7-11(17)9-12(13)21-10-16(18-20-21)19-26(22,23)15-6-4-3-5-14(15)25-2/h3-10,19H,1-2H3
Release date: 2024-09-11
Crystal Structure of human phosphodiesterase 10 in complex with 2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methylsulfanyl]-3H-imidazo[4,5-h]quinoline (PDB entry 5SHP)
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): 2.18
R work: 0.1868
R free: 0.2307
Average B factor: 39.744
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: 2.68
Solvent content (%): 54.08
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
Human APE1 K98A AP-endonuclease product complex (PDB entry 6P93)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 276 residues
Sequence: ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETACSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1719
R free: 0.2262
Average B factor: 29.093
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Matthews coefficient: 2.54
Solvent content (%): 51.58
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: 2020-01-01
Mimetic of UBC9-SUMO1 (PDB entry 8ODR)
Macromolecule: SUMO-conjugating enzyme UBC9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2
Sequence length: 165 residues
Sequence: MGHHHHHHSGIALSRLAQERRAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPKQAEAYTIYCQNRVEYEKRVRAQAKKFAPS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2212
R free: 0.2579
Average B factor: 65.45
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: LiSO4, Tris pH8.5, PEG 4000
Matthews coefficient: 2.29
Solvent content (%): 46.3
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: 2023-06-07
Crystal structure of SETD2 bound to histone H3.3 K36I peptide (PDB entry 5JLB)
Macromolecule: Histone-lysine N-methyltransferase SETD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 279 residues
Sequence: SGETSVPPGSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKKNKSHRDIKRMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGKMKKERSRK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1642
R free: 0.1903
Average B factor: 29.4487
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M KSCN, 0.1 M Bis-Tris Propane, 20% PEG3350
Matthews coefficient: 2.68
Solvent content (%): 54.07
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2016-11-02
Crystal structure of the kinase domain of the Q207E mutant of ACVR1 (ALK2) in complex with a 2-aminopyridine inhibitor K02288 (PDB entry 6EIX)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 340 residues
Sequence: SMTTNVGDSTLADLLDHSCTSGSGSGLPFLVQRTVAREITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKIDNSLDKLKTDC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.18825
R free: 0.24944
Average B factor: 33.214
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES pH 6.5 -- 12%(w/v) PEG 20000
Matthews coefficient: 2.21
Solvent content (%): 44.35
Ligand: 3-[6-amino-5-(3,4,5-trimethoxyphenyl)pyridin-3-yl]phenol (A3F)
Ligand formula: C20 H20 N2 O4
Ligand molecular weight: 352.384
Ligand SMILES: COc1cc(cc(c1OC)OC)c2cc(cnc2N)c3cccc(c3)O
Ligand InChI: InChI=1S/C20H20N2O4/c1-24-17-9-13(10-18(25-2)19(17)26-3)16-8-14(11-22-20(16)21)12-5-4-6-15(23)7-12/h4-11,23H,1-3H3,(H2,21,22)
Release date: 2017-09-27
Crystal Structure of human phosphodiesterase 10 in complex with 4-(azetidine-1-carbonyl)-2-methyl-N-(2-morpholin-4-yl-[1,2,4]triazolo[1,5-a]pyridin-7-yl)pyrazole-3-carboxamide (PDB entry 5SEH)
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): 2.1
R work: 0.1916
R free: 0.2343
Average B factor: 39.13
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: 2.65
Solvent content (%): 53.61
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
The crystal structure of mupain-1--16-IG in complex with murinised human uPA at pH7.4 (PDB entry 4ZHM)
Macromolecule: mupain-1-16-IG
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 10 residues
Sequence: CPAYSAYIGC
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.22343
R free: 0.26415
Average B factor: 40.003
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% polyethylene glycol (PEG) 400
Matthews coefficient: 2.06
Solvent content (%): 40.23
Ligand: piperidine-1-carboximidamide (MRZ)
Ligand formula: C6 H13 N3
Ligand molecular weight: 127.188
Ligand SMILES: C1CCN(CC1)C(=N)N
Ligand InChI: InChI=1S/C6H13N3/c7-6(8)9-4-2-1-3-5-9/h1-5H2,(H3,7,8)
Release date: 2015-09-16
Tankyrase 1 with Phthalazinone 2 (PDB entry 5EBT)
Macromolecule: Tankyrase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 210 residues
Sequence: MTILLDLAPEDKEYQSVEEEMQSTIREHRDGGNAGGIFNRYNVIRIQKVVNKKLRERFCHRQKEVSEENHNHHNERMLFHGSPFINAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPTHKDRSCYICHRQMLFCRVTLGKSFLQFSTIKMAHAPPGHHSVIGRPSVNGLAYAEYVIYRGEQAYPEYLITYQIMKPE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.171
R free: 0.2078
Average B factor: 30.05
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 298
Crystal growth procedure: 14% PEG 20K, 0.1 M PCPT pH5.8
Matthews coefficient: 2.44
Solvent content (%): 49.53
Ligand: (R,R)-2,3-BUTANEDIOL (BU3)
Ligand formula: C4 H10 O2
Ligand molecular weight: 90.121
Ligand SMILES: CC(C(C)O)O
Ligand InChI: InChI=1S/C4H10O2/c1-3(5)4(2)6/h3-6H,1-2H3/t3-,4-/m1/s1
Release date: 2016-03-02
Crystal Structure of the Vif-Binding Domain of Human APOBEC3F (PDB entry 3WUS)
Macromolecule: DNA dC->dU-editing enzyme APOBEC-3F
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4
Sequence length: 190 residues
Sequence: MNPILRNPMEAMYPHIFYFHFKNLRKAYGRNESWLCFTMEVVKHHSPVSWKRGVFRNQVDPETHCHAERCFLSWFCDDILSPNTNYEVTWYTSWSPCPECAGEVAEFLARHSNVNLTIFTARLYYFWDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPWKGLKYNFLFLDSKLQEILE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.54
R work: 0.19979
R free: 0.25648
Average B factor: 54.789
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 8.5% PEG 20000, 2% Dioxane, 300mM L-Arginine HCl, 85mM Na BICINE, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 3.43
Solvent content (%): 64.12
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: 2015-06-24
Crystal structure of DAPK1 in complex with 7,3',4'-trihydroxyisoflavone. (PDB entry 5AV0)
Macromolecule: Death-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 293 residues
Sequence: MTVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1868
R free: 0.2198
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2 M ammonium sulfate, 0.1 M MES
Matthews coefficient: 1.89
Solvent content (%): 34.95
Ligand: 3-(3,4-dihydroxyphenyl)-7-hydroxy-4H-chromen-4-one (47X)
Ligand formula: C15 H10 O5
Ligand molecular weight: 270.237
Ligand SMILES: c1cc(c(cc1C2=COc3cc(ccc3C2=O)O)O)O
Ligand InChI: InChI=1S/C15H10O5/c16-9-2-3-10-14(6-9)20-7-11(15(10)19)8-1-4-12(17)13(18)5-8/h1-7,16-18H
Release date: 2015-10-07
Crystal Structure of human phosphodiesterase 10 in complex with 2-chloro-5-methoxy-3-methylquinoxaline (PDB entry 5SK9)
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): 2.82
R work: 0.2123
R free: 0.2389
Average B factor: 81.42
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: 2.64
Solvent content (%): 53.4
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
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (R & S isomers), beta, gamma dATP analogue (PDB entry 6CR8)
Macromolecule: Template Strand
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 16 residues
Sequence: CCGACTGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1906
R free: 0.2483
Average B factor: 32.3015
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.26
Solvent content (%): 45.6
Ligand: 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyadenosine (VA4)
Ligand formula: C11 H17 Cl N5 O11 P3
Ligand molecular weight: 523.654
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(P(=O)(O)O)Cl)O)O)N
Ligand InChI: InChI=1S/C11H17ClN5O11P3/c12-11(29(19,20)21)30(22,23)28-31(24,25)26-2-6-5(18)1-7(27-6)17-4-16-8-9(13)14-3-15-10(8)17/h3-7,11,18H,1-2H2,(H,22,23)(H,24,25)(H2,13,14,15)(H2,19,20,21)/t5-,6+,7+,11+/m0/s1
Release date: 2018-07-04
Crystal structure of C4S3: A computationally designed immunogen to target Carbohydrate-Occluded Epitopes on the HIV envelope (PDB entry 6CBU)
Macromolecule: Acylphosphatase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.7
Sequence length: 100 residues
Sequence: GMAEGNTLISVDYEIFGKVQGVFFRKHTQAEGKKLGLVGWVQNTDRGTVQGQLQGPISKVRHMQEWLETRGSPKSHIDKANFNNEKLIEELDYSDFQIVA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.143
R free: 0.1532
Average B factor: 8.508
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG 3350, 200 mM Bis-tris, pH 6.5, 200 mM LiSO4
Matthews coefficient: 2.16
Solvent content (%): 43.17
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: 2019-02-06
NON-RECEPTOR PROTEIN TYROSINE PHOSPHATASE SHP2 IN COMPLEX WITH ALLOSTERIC INHIBITOR Isoxazolo-pyridinone 3 (PDB entry 6MD9)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 526 residues
Sequence: SMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.218
R free: 0.272
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 17% PEG3350, 200MM AMMONIUM PHOSPHATE
Matthews coefficient: 2.28
Solvent content (%): 46.01
Ligand: 3-(2-chlorophenyl)-6-{4-[(dimethylamino)methyl]phenyl}-5-methyl[1,2]oxazolo[4,5-c]pyridin-4(5H)-one (JEJ)
Ligand formula: C22 H20 Cl N3 O2
Ligand molecular weight: 393.866
Ligand SMILES: CN1C(=Cc2c(c(no2)c3ccccc3Cl)C1=O)c4ccc(cc4)CN(C)C
Ligand InChI: InChI=1S/C22H20ClN3O2/c1-25(2)13-14-8-10-15(11-9-14)18-12-19-20(22(27)26(18)3)21(24-28-19)16-6-4-5-7-17(16)23/h4-12H,13H2,1-3H3
Release date: 2019-02-13
Notum Fragment 916 (PDB entry 7BDB)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.1963
R free: 0.2107
Average B factor: 24.7256
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.97
Solvent content (%): 37.64
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: 2022-01-12
Dimer of Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence derived from human GLI1 gene (PDB entry 6VFF)
Macromolecule: Double-stranded RNA-specific editase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4.37
Sequence length: 488 residues
Sequence: GASLAQPPLPVLPPFPPPSGKNPVMILNELRPGLKYDFLSESGESHAKSFVMSVVVDGQFFEGSGRNKKLAKARAAQSALAAIFNLHLDQTPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGQGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLTP
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.1965
R free: 0.2483
Average B factor: 81.4
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: 50mM MOPS pH 7.0, 20% w/v PEG 4000, 100 mM NaCl
Matthews coefficient: 2.62
Solvent content (%): 53.08
Ligand: INOSITOL HEXAKISPHOSPHATE (IHP)
Ligand formula: C6 H18 O24 P6
Ligand molecular weight: 660.035
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C6H18O24P6/c7-31(8,9)25-1-2(26-32(10,11)12)4(28-34(16,17)18)6(30-36(22,23)24)5(29-35(19,20)21)3(1)27-33(13,14)15/h1-6H,(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3-,4+,5-,6-
Release date: 2020-07-01
Crystal structure of HDAC8 in complex with compound 2 (PDB entry 6ODA)
Macromolecule: Histone deacetylase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 413 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNAMEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVIEGRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.88
R work: 0.1988
R free: 0.24875
Average B factor: 56.341
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.3
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MES pH5.3, 5% PEG6000, 0.06M Gly-Gly-Gly, 4mM TCEP
Matthews coefficient: 2.69
Solvent content (%): 54.19
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: 2020-04-01
Crystal structure of human dual specificity phosphatase 1 catalytic domain (C258S) as a maltose binding protein fusion in complex with the monobody YSX1 (PDB entry 6APX)
Macromolecule: Maltose-binding periplasmic protein,Dual specificity protein phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Escherichia coli K-12
EC number: 3.1.3.16
Sequence length: 520 residues
Sequence: MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAGGPVEILPFLYLGSAYHASRKDMLDALGITALINVSANCPNHFEGHYQYKSIPVEDNHKADISSWFNEAIDFIDSIKNAGGRVFVHSQAGISRSATICLAYLMRTNRVKLDEAFEFVKQRRSIISPNFSFMGQLLQFESQVLAHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.491
R work: 0.2068
R free: 0.2365
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.9
Crystallization temperature (K): 292
Crystal growth procedure: 75 mM MES pH 5.9
2.4 M ammonium sulfate
Matthews coefficient: 3.76
Solvent content (%): 67.29
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: 2017-11-01