satarupa22/MacromolecularLigandDB huggingface dataset:
Caspase-3 Mutant - S150Y (PDB entry 6BGS)
Macromolecule: Caspase-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.56
Sequence length: 175 residues
Sequence: MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRYLTGKPKLFIIQACRGTELDCGIETD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1511
R free: 0.1769
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
Matthews coefficient: 2.15
Solvent content (%): 42.76
Release date: 2018-02-21
Human APE1 substrate complex with an A/A mismatch adjacent the THF (PDB entry 6BOQ)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 318 residues
Sequence: MPKRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.2174
R free: 0.2583
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Matthews coefficient: 2.29
Solvent content (%): 46.35
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: 2018-08-15
Crystal Structure of Human Cytochrome P450 2C9*27 (R150L) Genetic Variant in Complex with the Drug Losartan (PDB entry 8VZ7)
Macromolecule: Cytochrome P450 2C9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.1
Sequence length: 476 residues
Sequence: MAKKTSGRGKLPPGPTPLPVIGNILQIGIKDISKSLTNLSKVYGPVFTLYFGLKPIVVLHGYEAVKEALIDLGEEFSGRGIFPLAERANRGFGIVFSNGKKWKEIRRFSLMTLRNFGMGKRSIEDRVQEEALCLVEELRKTKASPCDPTFILGCAPCNVICSIIFHKRFDYKDQQFLNLMEKLNENIKILSSPWIQICNNFSPIIDYFPGTHNKLLKNVAFMKSYILEKVKEHQESMDMNNPQDFIDCFLMKMEKEKHNQPSEFTIESLENTAVDLFGAGTETTSTTLRYALLLLLKHPEVTAKVQEEIERVIGRNRSPCMQDRSHMPYTDAVVHEVQRYIDLLPTSLPHAVTCDIKFRNYLIPKGTTILISLTSVLHDNKEFPNPEMFDPHHFLDEGGNFKKSKYFMPFSAGKRICVGEALAGMELFLFLTSILQNFNLKSLVDPKNLDTTPVVNGFASVPPFYQLCFIPIHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.15092
R free: 0.21531
Average B factor: 60.981
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.3M Sodium Acetate Trihydrate
0.1 M Tris pH 7.5
25% w/v PEG 2000 MME
Matthews coefficient: 4
Solvent content (%): 69.29
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2024-06-12
Structure of DCN1 bound to NAcM-COV (PDB entry 5V88)
Macromolecule: Lysozyme,DCN1-like protein 1
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 384 residues
Sequence: MGSSHHHHHHSQDLENLYFQGSMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWAEAAVNLAKSRWYNQTPNRTKRVITTFATGTWDAYKNLRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.601
R work: 0.1593
R free: 0.1885
Average B factor: 35.9045
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 6% PEG3350, 0.2M NH4Br
Matthews coefficient: 2.26
Solvent content (%): 45.58
Ligand: N-{2-[({1-[(2R)-pentan-2-yl]piperidin-4-yl}{[3-(trifluoromethyl)phenyl]carbamoyl}amino)methyl]phenyl}propanamide (8ZD)
Ligand formula: C28 H37 F3 N4 O2
Ligand molecular weight: 518.614
Ligand SMILES: CCCC(C)N1CCC(CC1)N(Cc2ccccc2NC(=O)CC)C(=O)Nc3cccc(c3)C(F)(F)F
Ligand InChI: InChI=1S/C28H37F3N4O2/c1-4-9-20(3)34-16-14-24(15-17-34)35(19-21-10-6-7-13-25(21)33-26(36)5-2)27(37)32-23-12-8-11-22(18-23)28(29,30)31/h6-8,10-13,18,20,24H,4-5,9,14-17,19H2,1-3H3,(H,32,37)(H,33,36)/t20-/m1/s1
Release date: 2017-05-24
IRAK4 IN COMPLEX WITH inhibitor (PDB entry 6TI8)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 308 residues
Sequence: GENKSLEVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.32
R work: 0.249
R free: 0.281
Average B factor: 68.53
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 2.7 M AMS 0.1 M Hepes pH 7.1-7.7  
Protein Buffer:  25 mM HEPES pH 7.5, 1 mM EDTA, 1 mM TCEP, 5% Glycerol, 150 mM NaCl
Matthews coefficient: 2.53
Solvent content (%): 51.36
Ligand: ~{N},~{N}-dimethyl-4-(1-methylcyclopropyl)oxy-2-[[1-(1-methylpiperidin-4-yl)pyrazol-4-yl]amino]pyrido[3,2-d]pyrimidine-6-carboxamide (NBW)
Ligand formula: C23 H30 N8 O2
Ligand molecular weight: 450.537
Ligand SMILES: CC1(CC1)Oc2c3c(ccc(n3)C(=O)N(C)C)nc(n2)Nc4cnn(c4)C5CCN(CC5)C
Ligand InChI: InChI=1S/C23H30N8O2/c1-23(9-10-23)33-20-19-17(5-6-18(26-19)21(32)29(2)3)27-22(28-20)25-15-13-24-31(14-15)16-7-11-30(4)12-8-16/h5-6,13-14,16H,7-12H2,1-4H3,(H,25,27,28)
Release date: 2020-10-28
Crystal structure of KRAS4a (GMPPNP) in complex with RAF1 (RBD) (PDB entry 8T74)
Macromolecule: RAF proto-oncogene serine/threonine-protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 80 residues
Sequence: SKTSNTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKARLDWNTDAASLIGEELQVDFL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1728
R free: 0.1958
Average B factor: 42.6345
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.15 M DL-malic acid (pH 7.0), 20% PEG 3350
Matthews coefficient: 2.48
Solvent content (%): 50.44
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: 2024-02-14
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with RK4-337 (PDB entry 5QHC)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.1886
R free: 0.2282
Average B factor: 41.295
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.4
Solvent content (%): 72.05
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: 2019-03-27
Crystal structure of VASH 2 in complex with SVBP (PDB entry 6QBY)
Macromolecule: Tubulinyl-Tyr carboxypeptidase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.17
Sequence length: 257 residues
Sequence: MEEDKDGGVLFHVNKSGFPIDSHTWERMWMHVAKVHPKGGEMVGAIRNAAFLAKPSIPQVPNYRLSMTIPDWLQAIQNYMKTLQYNHTGTQFFEIRKMRPLSGLMETAKEMTRESLPIKCLEAVILGIYLTNGQPSIERFPISFKTYFSGNYFHHVVLGIYCNGRYGSLGMSRRAELMDKPLTFRTLSDLIFDFEDSYKKYLHTVKKVKIGLYVPHEPHSFQPIEWKQLVLNVSKMLRADIRKELEKYARDMRMKIL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.19
R free: 0.23
Average B factor: 53.52
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.2M Sodium formate
0.1M Bis-Tris propane pH 6.5
20% PEG3350
Matthews coefficient: 2.74
Solvent content (%): 60
Release date: 2019-04-24
Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(3-chlorobenzyl)pyrrolidine-2-carboxamide (PDB entry 5MLS)
Macromolecule: Thrombin light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62
R work: 0.16
R free: 0.18
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM Sodium dihydrogen phosphate ph 7.5, 350 mM NaCl, 27% PEG 8000
Matthews coefficient: 2.5
Solvent content (%): 51.1
Ligand: D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide (22U)
Ligand formula: C21 H24 Cl N3 O2
Ligand molecular weight: 385.887
Ligand SMILES: c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NCc3cccc(c3)Cl)N
Ligand InChI: InChI=1S/C21H24ClN3O2/c22-17-9-4-8-16(12-17)14-24-20(26)19-10-5-11-25(19)21(27)18(23)13-15-6-2-1-3-7-15/h1-4,6-9,12,18-19H,5,10-11,13-14,23H2,(H,24,26)/t18-,19+/m1/s1
Release date: 2017-12-20
Structure of the HOIP PUB domain bound to SPATA2 PIM peptide (PDB entry 5LJN)
Macromolecule: E3 ubiquitin-protein ligase RNF31
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 173 residues
Sequence: GEEERAFLVAREELASALRRDSGQAFSLEQLRPLLASSLPLAARYLQLDAARLVRCNAHGEPRNYLNTLSTALNILEKYGRNLLSPQRPRYWRGVKFNNPVFRSTVDAVQGGRDVLRLYGYTEEQPDGLSFPEGQEEPDEHQVATVTLEVLLLRTELSLLLQNTHPRQQALEQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.701
R work: 0.2325
R free: 0.2805
Average B factor: 61.8122
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.7-1.9 M (NH4)2SO4, 50 mM sodium cacodylate pH 6.4-7.0, 15 mM MgCl2

Protein:precipitant ratio; 1:2
200 nl drops
Matthews coefficient: 2.69
Solvent content (%): 54.31
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: 2016-08-24
Crystal structure of human Cathepsin-S with bound ligand (PDB entry 5QC4)
Macromolecule: Cathepsin S
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.27
Sequence length: 223 residues
Sequence: ILPDSVDWREKGCVTEVKYQGSCGASWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEILQGGG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.152
R free: 0.21
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Matthews coefficient: 2.07
Solvent content (%): 40.54
Ligand: 2-[5-[5-ethanoyl-1-[(2~{R})-2-oxidanyl-3-[4-(2-oxidanylpropan-2-yl)piperidin-1-yl]propyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]-2-(trifluoromethyl)phenyl]sulfanyl-1-pyrrolidin-1-yl-ethanone (BC7)
Ligand formula: C32 H44 F3 N5 O4 S
Ligand molecular weight: 651.783
Ligand SMILES: CC(=O)N1CCc2c(c(nn2CC(CN3CCC(CC3)C(C)(C)O)O)c4ccc(c(c4)SCC(=O)N5CCCC5)C(F)(F)F)C1
Ligand InChI: InChI=1S/C32H44F3N5O4S/c1-21(41)39-15-10-27-25(19-39)30(36-40(27)18-24(42)17-37-13-8-23(9-14-37)31(2,3)44)22-6-7-26(32(33,34)35)28(16-22)45-20-29(43)38-11-4-5-12-38/h6-7,16,23-24,42,44H,4-5,8-15,17-20H2,1-3H3/t24-/m1/s1
Release date: 2017-12-20
A multiconformer ligand model of 5T5 bound to BACE-1 (PDB entry 6DMI)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 390 residues
Sequence: RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVASIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1924
R free: 0.2258
Average B factor: 34.4303
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.5M SODIUM FORMATE, 100MM HEPES
Matthews coefficient: 2.96
Solvent content (%): 58.38
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-12-19
Binary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dC (PDB entry 8VFG)
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): 1.54
R work: 0.2006
R free: 0.2365
Average B factor: 20.76
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
Matthews coefficient: 2.43
Solvent content (%): 49.44
Release date: 2024-05-08
Human Carbonic anhydrase II mutant T199V bound by 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide (PDB entry 6RMY)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTVPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1646
R free: 0.2049
Average B factor: 16.721
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 0.1M sodium BICINE (pH 9) and 2M sodium malonate (pH 7).
Matthews coefficient: 2.09
Solvent content (%): 41.16
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: 2020-06-03
Inhibitor Complex with Thrombin Activatable Fibrinolysis Inhibitor (TAFIa) (PDB entry 7NEU)
Macromolecule: Carboxypeptidase B2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.20
Sequence length: 400 residues
Sequence: QSGQVLAALPRTSRQVQVLQNLTTTYEIVLWQPVTADLIVKKKQVHFFVNASDVDNVKAHLNVSGIPCSVLLADVEDLIQQQISNDTVSPRASASYYEQYHSLNEIYSWIEFITERHPDMLTKIHIGSSFEKYPLYVLKVSGKEQTAKNAIWIDCGIHAREWISPAFCLWFIGHITQFYGIIGQYTNLLRLVDFYVMPVVNVDGYDYSWKKNRMWRKNRSFYANNHCIGTDLNRNFASKHWCEEGASSSSCSETYCGLYPESEPEVKAVASFLRRNINQIKAYISMHSYSQHIVFPYSYTRSKCKDHEELSLVASEAVRAIEKISKNIRYTYGQGSETLYLAPGGGDDWIYDLGIKYSFTIELRDTGTYGFLLPERYIKPTCREAFAAVSKIAWHVIRNV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2012
R free: 0.2817
Average B factor: 30.706
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.25
Crystallization temperature (K): 293
Crystal growth procedure: 100mM MES, 300mM Ammonium Chloride, 35% PEG 3350
Matthews coefficient: 2.74
Solvent content (%): 55.14
Ligand: (1R,3S)-3-(4-ammoniobutyl)-1-(4-fluoro-2-(1-methyl-1H-imidazol-5-yl)benzyl)-1,4-azaphosphinan-1-ium-3-carboxylate 4,4-dioxide (U9K)
Ligand formula: C20 H30 F N4 O4 P
Ligand molecular weight: 440.449
Ligand SMILES: Cn1cncc1c2cc(ccc2C[NH+]3CCP(=O)(C(C3)(CCCC[NH3+])C(=O)O)O)F
Ligand InChI: InChI=1S/C20H28FN4O4P/c1-24-14-23-11-18(24)17-10-16(21)5-4-15(17)12-25-8-9-30(28,29)20(13-25,19(26)27)6-2-3-7-22/h4-5,10-11,14H,2-3,6-9,12-13,22H2,1H3,(H,26,27)(H,28,29)/p+2/t20-/m0/s1
Release date: 2021-04-07
Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with IACS-8968 (PDB entry 7M7D)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 411 residues
Sequence: MHHHHHHSSGLVPRGSHMISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2088
R free: 0.2352
Average B factor: 85.15
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris pH 8.0, 18% (w/v) PEG6000, 0.2 M NaCl
Matthews coefficient: 2.74
Solvent content (%): 55.12
Ligand: (5S)-6,6-dimethyl-8-[(4S)-7-(trifluoromethyl)imidazo[1,5-a]pyridin-5-yl]-1,3,8-triazaspiro[4.5]decane-2,4-dione (YRM)
Ligand formula: C17 H18 F3 N5 O2
Ligand molecular weight: 381.352
Ligand SMILES: CC1(CN(CCC12C(=O)NC(=O)N2)c3cc(cc4n3cnc4)C(F)(F)F)C
Ligand InChI: InChI=1S/C17H18F3N5O2/c1-15(2)8-24(4-3-16(15)13(26)22-14(27)23-16)12-6-10(17(18,19)20)5-11-7-21-9-25(11)12/h5-7,9H,3-4,8H2,1-2H3,(H2,22,23,26,27)/t16-/m1/s1
Release date: 2021-09-01
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000089a (PDB entry 5QDR)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.784
R work: 0.1842
R free: 0.2128
Average B factor: 41.7242
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.34
Solvent content (%): 63.12
Ligand: methyl 3-(methylsulfonylamino)benzoate (6SU)
Ligand formula: C9 H11 N O4 S
Ligand molecular weight: 229.253
Ligand SMILES: COC(=O)c1cccc(c1)NS(=O)(=O)C
Ligand InChI: InChI=1S/C9H11NO4S/c1-14-9(11)7-4-3-5-8(6-7)10-15(2,12)13/h3-6,10H,1-2H3
Release date: 2018-10-10
Human Carbonic anhydrase II bound by 3,5-dimethylbenzenesulfonamide (PDB entry 6T4O)
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): 1.133
R work: 0.1389
R free: 0.1661
Average B factor: 15.297
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate
Matthews coefficient: 2.08
Solvent content (%): 40.93
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-10-14
Structure of human DNA polymerase beta 279NA mutant complexed with G in the template base paired with incoming non-hydrolyzable CTP (PDB entry 4Z6C)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 16 residues
Sequence: CCGACGTCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.677
R work: 0.2006
R free: 0.2723
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.12
Solvent content (%): 42
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: 2016-04-13