satarupa22/MacromolecularLigandDB huggingface dataset:
Ternary complex of DNA polymerase Mu with 1-nt gapped DNA (T:dGMPNPP) and Mg (PDB entry 7CO9)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 482 residues
Sequence: MLPKRRRARVGSPSGDAASSTPPSTRFPGVAIYLVEPRMGRSRRAFLTGLARSKGFRVLDACSSEATHVVMEETSAEEAVSWQERRMAAAPPGCTPPALLDISWLTESLGAGQPVPVECRHRLEVAGPRKGPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.599
R work: 0.1707
R free: 0.1962
Average B factor: 26.8194
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: TRIS-HCL, PEG 3350
Matthews coefficient: 1.94
Solvent content (%): 36.49
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: 2021-06-30
hMiro1 C-domain GDP Complex P41212 Crystal Form (PDB entry 5KSY)
Macromolecule: Mitochondrial Rho GTPase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 192 residues
Sequence: MGKKQTQRNVFRCNVIGVKNCGKSGVLQALLGRNLMRQKKIREDHKSYYAINTVYVYGQEKYLLLHDISESEFLTEAEIICDVVCLVYDVSNPKSFEYCARIFKQHFMDSRIPCLIVAAKSDLHEVKQEYSISPTDFCRKHKMPPPQAFTCNTADAPSKDIFVKLTTMAMYPHVTQADLKSSTFLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.482
R work: 0.2659
R free: 0.3149
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 294
Crystal growth procedure: 12 mg/mL protein, 0.1 M Tris, pH 8.5, 16% w/v PEG10000, GDP observed in the structure was carried through from the expression system during purification
Matthews coefficient: 2.29
Solvent content (%): 46.34
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2016-09-21
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase (PDB entry 5I9U)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.889
R work: 0.1631
R free: 0.2244
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 37.5 % MPD_P1k_P3350, 0.1 M Amino Acids, 0.1 M Bicine/Trizma base pH 8.5
Matthews coefficient: 1.97
Solvent content (%): 37.6
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: 2016-11-09
The crystal structure of the intact human GlnRS (PDB entry 4YE6)
Macromolecule: Glutamine--tRNA ligase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.18
Sequence length: 776 residues
Sequence: HMAALDSLSLFTSLGLSEQKARETLKNSALSAQLREAATQAQQTLGSTIDKATGILLYGLASRLRDTRRLSFLVSYIASKKIHTEPQLSAALEYVRSHPLDPIDTVDFERECGVGVIVTPEQIEEAVEAAINRHRPQLLVERYHFNMGLLMGEARAVLKWADGKMIKNEVDMQVLHLLGPKLEADLEKKFKVAKARLEETDRRTAKDVVENGETADQTLSLMEQLRGEALKFHKPGENYKTPGYVVTPHTMNLLKQHLEITGGQVRTRFPPEPNGILHIGHAKAINFNFGYAKANNGICFLRFDDTNPEKEEAKFFTAICDMVAWLGYTPYKVTYASDYFDQLYAWAVELIRRGLAYVCHQRGEELKGHNTLPSPWRDRPMEESLLLFEAMRKGKFSEGEATLRMKLVMEDGKMDPVAYRVKYTPHHRTGDKWCIYPTYDYTHCLCDSIEHITHSLCTKEFQARRSSYFWLCNALDVYCPVQWEYGRLNLHYAVVSKRKILQLVATGAVRDWDDPRLFTLTALRRRGFPPEAINNFCARVGVTVAQTTMEPHLLEACVRDVLNDTAPRAMAVLESLRVIITNFPAAKSLDIQVPNFPADETKGFHQVPFAPIVFIERTDFKEEPEPGFKRLAWGQPVGLRHTGYVIELQHVVKGPSGCVESLEVTCRRADAGEKPKAFIHWVSQPLMCEVRLYERLFQHKNPEDPTEVPGGFLSDLNLASLHVVDAALVDCSVALAKPFDKFQFERLGYFSVDPDSHQGKLVFNRTVTLKEDPGKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2105
R free: 0.2391
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 289.15
Crystal growth procedure: 0.1M calcium acetate, 0.1M Tris, pH 6.0, 12.5% (w/v) PEG 3,350, 60mM gly-gly-gly
Matthews coefficient: 4.73
Solvent content (%): 74
Release date: 2016-02-17
Human PTPRU D1 domain, oxidised form (PDB entry 6SUC)
Macromolecule: Receptor-type tyrosine-protein phosphatase U
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 297 residues
Sequence: MGSSHHHHHHTGGTHPAVRVADLLQHINQMKTAEGYGFKQEYESFFEGWDATKKKDKVKGSRQEPMPAYDRHRVKLHPMLGDPSADYINANYIDGYHRSNHFIATQGPKPEMVYDFWRMVWQEHCSSIVMITKLVEVGRVKCSRYWPEDSDTYGDIKIMLVKTETLAEYVVRTFALERRGYSARHEVRQFHFTAWPEHGVPYHATGLLAFIRRVKASTPPDAGPIVIHCSAGTGRTGCYIVLDVMLDMAECEGVVDIYNCVKTLCSRRVNMIQTEEQYIFIHDAILEACLCGETTIP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.2139
R free: 0.2452
Average B factor: 37.35
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M BICINE, pH 9, 1 M lithium chloride, 20% (w/v) polyethylene glycol 6000
Matthews coefficient: 2.69
Solvent content (%): 54.21
Release date: 2020-07-08
Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with the negative allosteric modulator 3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile - (HTL14242) (PDB entry 5CGD)
Macromolecule: Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 444 residues
Sequence: AASPVQYLRWGDPAPIAAVVFACLGLLATLFVTVVFIIYRDTPVVKSSSRELCYIILAGICLGYLCTFCLIAKPKQIYCYLQRIGIGLSPAMSYSALVTKTYRAARILAMSKKNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKICTKKPRFMSACAQLVIAFILICIQLGIIVALFIMEPPDIMHDYPSIREVYLICNTTNLGVVAPLGYNGLLILACTFYAFKTRNVPANFNEAKYIAFTMYTTCIIWLAFVPIYFGSNYKIITMCFSVSLSATVALGCMFVPKVYIILAKPERNVRSAAAAHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.603
R work: 0.2419
R free: 0.2853
Average B factor: 37
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 6.8
Crystallization temperature (K): 293.1
Crystal growth procedure: 24-34% V/V PEG400, 0.2 M AMMONIUM  PHOSPHATE DIBASIC, 0.1 M MES, PH 6.8,
Matthews coefficient: 2.53
Solvent content (%): 51.37
Ligand: OLEIC ACID (OLA)
Ligand formula: C18 H34 O2
Ligand molecular weight: 282.461
Ligand SMILES: CCCCCCCCC=CCCCCCCCC(=O)O
Ligand InChI: InChI=1S/C18H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h9-10H,2-8,11-17H2,1H3,(H,19,20)/b10-9-
Release date: 2015-08-12
JAK2 JH1 in complex with MA9-086 (PDB entry 6VNF)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 308 residues
Sequence: HHHHHHHHENLYFQGDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.1929
R free: 0.2221
Average B factor: 61.1712
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% PEG 3350
Matthews coefficient: 3.03
Solvent content (%): 59.38
Ligand: N~4~-[1-(tert-butylsulfonyl)-2,3-dihydro-1H-indol-6-yl]-N~2~-[3-fluoro-4-(1-methylpiperidin-4-yl)phenyl]-5-methylpyrimidine-2,4-diamine (R6S)
Ligand formula: C29 H37 F N6 O2 S
Ligand molecular weight: 552.706
Ligand SMILES: Cc1cnc(nc1Nc2ccc3c(c2)N(CC3)S(=O)(=O)C(C)(C)C)Nc4ccc(c(c4)F)C5CCN(CC5)C
Ligand InChI: InChI=1S/C29H37FN6O2S/c1-19-18-31-28(33-22-8-9-24(25(30)16-22)20-10-13-35(5)14-11-20)34-27(19)32-23-7-6-21-12-15-36(26(21)17-23)39(37,38)29(2,3)4/h6-9,16-18,20H,10-15H2,1-5H3,(H2,31,32,33,34)
Release date: 2021-02-17
Crystal Structure of DDX3X449_450ET>DP (PDB entry 7YMF)
Macromolecule: ATP-dependent RNA helicase DDX3X
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 178 residues
Sequence: ITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVDPKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYEHHYKGSSLEHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1852
R free: 0.244
Average B factor: 34.01
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 6.5, 1.5 M Sodium Formate , 50 mM Magnesium chloride
Matthews coefficient: 2.34
Solvent content (%): 47.51
Release date: 2024-01-03
DGY-06-116, a novel and selective covalent inhibitor of SRC kinase (PDB entry 6E6E)
Macromolecule: Proto-oncogene tyrosine-protein kinase Src
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 276 residues
Sequence: DAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGETGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGENL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.2499
R free: 0.2849
Average B factor: 46.64
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Magnesium Formate Dihydrate; 15% PEG3350
Matthews coefficient: 2.53
Solvent content (%): 51.44
Ligand: N-(2-chloro-6-methylphenyl)-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-4-{[2-(propanoylamino)phenyl]amino}pyrimidine-5-carboxamide (HVY)
Ligand formula: C32 H35 Cl N8 O2
Ligand molecular weight: 599.126
Ligand SMILES: CCC(=O)Nc1ccccc1Nc2c(cnc(n2)Nc3ccc(cc3)N4CCN(CC4)C)C(=O)Nc5c(cccc5Cl)C
Ligand InChI: InChI=1S/C32H35ClN8O2/c1-4-28(42)36-26-10-5-6-11-27(26)37-30-24(31(43)38-29-21(2)8-7-9-25(29)33)20-34-32(39-30)35-22-12-14-23(15-13-22)41-18-16-40(3)17-19-41/h5-15,20H,4,16-19H2,1-3H3,(H,36,42)(H,38,43)(H2,34,35,37,39)
Release date: 2019-07-31
Crystal structure of Human Peroxisomal coenzyme A diphosphatase NUDT7 (PDB entry 5T3P)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 236 residues
Sequence: SMSRLGLPEEPVRNSLLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPTFEVQFNLNDVLASSEELFLKVHKKAT
Oligomeric state: Homo 3-mer
Stoichiometry: A3
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.1774
R free: 0.225
Average B factor: 51.3431
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.8M Sodium phosphate monobasic, 0.8M pottassium phosphate dibasic, 0.1M HEPES pH 7.5
Matthews coefficient: 2.68
Solvent content (%): 54.18
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: 2017-09-13
Crystal structure of the ALK kinase domain in complex with Entrectinib (PDB entry 5FTO)
Macromolecule: ALK TYROSINE KINASE RECEPTOR
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 315 residues
Sequence: GPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.19605
R free: 0.25701
Average B factor: 25.973
Crystallization pH: 8.5
Crystal growth procedure: 18% PEG3350, 0.1 M TRIS/HCL PH 8.5
Matthews coefficient: 2.3
Solvent content (%): 47
Ligand: Entrectinib (YMX)
Ligand formula: C31 H34 F2 N6 O2
Ligand molecular weight: 560.637
Ligand SMILES: CN1CCN(CC1)c2ccc(c(c2)NC3CCOCC3)C(=O)Nc4c5cc(ccc5[nH]n4)Cc6cc(cc(c6)F)F
Ligand InChI: InChI=1S/C31H34F2N6O2/c1-38-8-10-39(11-9-38)25-3-4-26(29(19-25)34-24-6-12-41-13-7-24)31(40)35-30-27-17-20(2-5-28(27)36-37-30)14-21-15-22(32)18-23(33)16-21/h2-5,15-19,24,34H,6-14H2,1H3,(H2,35,36,37,40)
Release date: 2016-04-06
Crystal Structure of human phosphodiesterase 10 in complex with N-[1-methyl-5-(methylcarbamoyl)pyrazol-4-yl]-6-[(3S)-oxolan-3-yl]-3-(pyrimidin-5-ylamino)pyrazine-2-carboxamide (PDB entry 5SKK)
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): 2.15
R work: 0.1902
R free: 0.2421
Average B factor: 45.353
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: 2.62
Solvent content (%): 53.05
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
RNF38-UB-UbcH5B-Ub complex (PDB entry 4V3L)
Macromolecule: UBIQUITIN-CONJUGATING ENZYME E2 D2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2.19
Sequence length: 146 residues
Sequence: ALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.1828
R free: 0.1926
Average B factor: 31.1
Crystal growth procedure: 50 MM HEPES, PH 7.5, 0.2 M MAGNESIUM ACETATE AND 13% (W/V) PEG 8K
Matthews coefficient: 2.5
Solvent content (%): 50.72
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: 2015-04-08
Human renin in complex with compound1 (PDB entry 7XGK)
Macromolecule: Renin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.15
Sequence length: 340 residues
Sequence: LTLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2017
R free: 0.2451
Average B factor: 52.785
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 50mM Na citrate pH4.5, 18-26% PEG3350, 0.6M NaCl
Matthews coefficient: 3.16
Solvent content (%): 61.04
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2022-08-31
BIFUNCTIONAL INHIBITION OF NEUTROPHIL ELASTASE AND CATHEPSIN G by Eap3 of S. aureus (PDB entry 9ASX)
Macromolecule: Cathepsin-G
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 223 residues
Sequence: IIGGRESRPHSRPYMAYLQIQSPAGQSRCGGFLVREDFVLTAAHCWGSNINVTLGAHNIQRRENTQQHITARRAIRHPQYNQRTIQNDIMLLQLSRRVRRNRNVNPVALPRAQEGLRPGTLCTVAGWGRVSMRRGTDTLREVQLRVQRDRQCLRIFGSYDPRRQICVGDRRERKAAFKGDSGGPLLCNNVAHGIVSYGKSSGVPPEVFTRVSSFLPWIRTTMR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1926
R free: 0.2284
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M  ammonium citrate
0.1 M  imidazole (pH 6.8)
22% (w/v) peg-2kMME
Matthews coefficient: 2.36
Solvent content (%): 47.85
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2024-06-12
Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with D-3-deoxy-myo-inositol 1,4,6-trisphosphate/ATP/Mn (PDB entry 8PPB)
Macromolecule: Inositol-trisphosphate 3-kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.127
Sequence length: 279 residues
Sequence: GSHMSWVQLAGHTGSFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.19467
R free: 0.21606
Average B factor: 38.798
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.84 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. 
Protein:precipitant ratio 1:1. 
Protein concentration: 18 mg/ml. 
Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. 
Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ATP and 3 mM MnCl2.
Matthews coefficient: 2.68
Solvent content (%): 54.11
Ligand: D-3-deoxy-myo-inositol 1,4,6-trisphosphate (3I2)
Ligand formula: C6 H15 O14 P3
Ligand molecular weight: 404.096
Ligand SMILES: C1C(C(C(C(C1OP(=O)(O)O)O)OP(=O)(O)O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C6H15O14P3/c7-2-1-3(18-21(9,10)11)4(8)6(20-23(15,16)17)5(2)19-22(12,13)14/h2-8H,1H2,(H2,9,10,11)(H2,12,13,14)(H2,15,16,17)/t2-,3-,4+,5-,6-/m1/s1
Release date: 2024-02-28
PKAB3 in complex with pyrrolidine inhibitor 34a (PDB entry 4Z84)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Bos taurus
EC number: 2.7.11.11
Sequence length: 351 residues
Sequence: MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYAPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLMIDQQGYIKVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.554
R work: 0.208221335319
R free: 0.23429993529
Average B factor: 29.9211444025
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: The droplets, containing 16 mg/ml protein 25 mM Bis-Tris-HCl, pH 7.0, 150 mM KCl, 1.5mM octanoyl-N-methylglucamide, 0.8 mM PKI peptide and 1mM of the pyrrolidine  inhibitor 34a, were equilibrated against 12-26 % (v/v) methanol.
Matthews coefficient: 2.31
Solvent content (%): 46.83
Ligand: 7-[(3S,4R)-4-(3-chlorophenyl)carbonylpyrrolidin-3-yl]-3H-quinazolin-4-one (NVX)
Ligand formula: C19 H16 Cl N3 O2
Ligand molecular weight: 353.802
Ligand SMILES: c1cc(cc(c1)Cl)C(=O)C2CNCC2c3ccc4c(c3)N=CNC4=O
Ligand InChI: InChI=1S/C19H16ClN3O2/c20-13-3-1-2-12(6-13)18(24)16-9-21-8-15(16)11-4-5-14-17(7-11)22-10-23-19(14)25/h1-7,10,15-16,21H,8-9H2,(H,22,23,25)/t15-,16+/m1/s1
Release date: 2015-12-02
Structure of Calcineurin bound to RCAN1 (PDB entry 6UUQ)
Macromolecule: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 316 residues
Sequence: MGSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESVALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMDAFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFGNEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.849
R work: 0.1635
R free: 0.2049
Average B factor: 24.993
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Sodium cacodylate, 12% Peg 8000, 0.1 M Calcium acetate
Matthews coefficient: 2.32
Solvent content (%): 47
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2020-09-09