satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda with an 8-oxo-dG:dC base-pair (PDB entry 5IIN)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 334 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1872
R free: 0.2314
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 0.2 M ammonium acetate, 0.1 M sodium citrate pH 4.8, and 3-5% PEG 4000
Matthews coefficient: 2.89
Solvent content (%): 57.41
Ligand: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE (DUP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
Release date: 2016-08-17
Human sterol 14 alpha-demethylase (CYP51) in complex with the reaction intermediate 14 alpha-aldehyde dihydrolanosterol (PDB entry 8SS0)
Macromolecule: Lanosterol 14-alpha demethylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.154
Sequence length: 458 residues
Sequence: MAKKTSSKGKLPPYIFSPIPFLGHAIAFGKSPIEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEDVYSRLTTPVFGKGVAYDVPNPVFLEQKKMLKSGLNIAHFKQHVSIIEKETKEYFESWGESGEKNVFEALSELIILTASHCLHGKEIRSQLNEKVAQLYADLAGGFSHAAWLLPGWLPLPSFRRRDRAHREIKDIFYKAIQKRRQSQEKIDDILQTLLDATYKDGRPLTDDEVAGMLIGLLLAGQATSSTTSAWMGFFLARDKTLQKKCYLEQKTVCGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIMMRMARTPQTVAGYTIPPGHQVCVSPTVNQRLKDSWVERLDFNPDRYLQDNPASGEKFAYVPFGAGRHRCIGENFAYVQIKTIWSTMLRLYEFDLIDGYFPTVNYTTMIHTPENPVIRYKRRSKHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.219
R free: 0.249
Average B factor: 37.13
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 290
Crystal growth procedure: CALCIUM ACATATE, PEG 4000, ANAPOE 80, 14 ALPHA ALDEHYDE DERIVATIVE OD DIHYDROLANOSTEROL
Matthews coefficient: 3.83
Solvent content (%): 67.85
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: 2024-01-17
High resolution crystal structure of human DDAH-1 in complex with N-(4-Aminobutyl)-N'-(2-Methoxyethyl)guanidine (PDB entry 6SZP)
Macromolecule: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.3.18
Sequence length: 297 residues
Sequence: MRGSHHHHHHGSMAGLGHPAAFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTCCSVLINKKVDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.2006
R free: 0.2303
Average B factor: 36.0639
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: reservoir: 0.1M MES pH 6.0 + 30% PEG6000
drop: 1+1 (v/v)
cryo protectant: reservoir + 20%(v/v) glycerol
Matthews coefficient: 2.12
Solvent content (%): 42.08
Ligand: (1~{S})-~{N}'-(4-azanylbutyl)-~{N}"-(2-methoxyethyl)methanetriamine (M3B)
Ligand formula: C8 H22 N4 O
Ligand molecular weight: 190.286
Ligand SMILES: COCCNC(N)NCCCCN
Ligand InChI: InChI=1S/C8H22N4O/c1-13-7-6-12-8(10)11-5-3-2-4-9/h8,11-12H,2-7,9-10H2,1H3/t8-/m0/s1
Release date: 2019-12-25
Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound BI-9564 (PDB entry 6TN8)
Macromolecule: Activin receptor type I
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.2278
R free: 0.2624
Average B factor: 42.02
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 1.6M ammonium sulfate, 10%(v/v) dioxane, 0.1M MES pH 6.5
Matthews coefficient: 2.65
Solvent content (%): 53.57
Ligand: 1,4-DIETHYLENE DIOXIDE (DIO)
Ligand formula: C4 H8 O2
Ligand molecular weight: 88.105
Ligand SMILES: C1COCCO1
Ligand InChI: InChI=1S/C4H8O2/c1-2-6-4-3-5-1/h1-4H2
Release date: 2019-12-18
FGFR4 complex with a covalent inhibitor (PDB entry 7DTZ)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: LLAGLVSLDLPLDPLWEFPRDRLVLGKPLGEGAFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDEVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.01
R work: 0.1651
R free: 0.1976
Average B factor: 22.4882
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Bis-Tris, 20% PEG 3350, 0.2M LiSO4, pH 4.5
Matthews coefficient: 2.32
Solvent content (%): 46.99
Ligand: N-[2-[[5-[[2,6-bis(chloranyl)-3,5-dimethoxy-phenyl]methoxy]pyrimidin-2-yl]amino]-3-methyl-phenyl]-2-fluoranyl-prop-2-enamide (HHL)
Ligand formula: C23 H21 Cl2 F N4 O4
Ligand molecular weight: 507.342
Ligand SMILES: Cc1cccc(c1Nc2ncc(cn2)OCc3c(c(cc(c3Cl)OC)OC)Cl)NC(=O)C(=C)F
Ligand InChI: InChI=1S/C23H21Cl2FN4O4/c1-12-6-5-7-16(29-22(31)13(2)26)21(12)30-23-27-9-14(10-28-23)34-11-15-19(24)17(32-3)8-18(33-4)20(15)25/h5-10H,2,11H2,1,3-4H3,(H,29,31)(H,27,28,30)
Release date: 2021-04-14
Structure of RNF31 in complex with FP06649, a Helicon Polypeptide (PDB entry 7UY2)
Macromolecule: E3 ubiquitin-protein ligase RNF31
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 184 residues
Sequence: GPLGSMPGEEEERAFLVAREELASALRRDSGQAFSLEQLRPLLASSLPLAARYLQLDAARLVRCNAHGEPRNYLNTLSTALNILEKYGRNLLSPQRPRYWRGVKFNNPVFRSTVDAVQGGRDVLRLYGYTEEQPDGLSFPEGQEEPDEHQVATVTLEVLLLRTELSLLLQNTHPRQQALEQLLE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.2114
R free: 0.2701
Average B factor: 61.82
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.06 M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate), 0.1 M Buffer System 1 (Imidazole; MES monohydrate (acid) pH 6.5), 37.5% Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
Matthews coefficient: 2.11
Solvent content (%): 41.72
Ligand: AMINO GROUP (NH2)
Ligand formula: H2 N
Ligand molecular weight: 16.023
Ligand SMILES: [NH2]
Ligand InChI: InChI=1S/H3N/h1H3
Release date: 2022-12-28
Human carbonic anhydrase II (F131Y/L198A) complexed with benzo[d]thiazole-2-sulfonamide (PDB entry 5JGS)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDYGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSATTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.11
R work: 0.1189
R free: 0.1314
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: We soaked monoclinic crystals of HCAII with BTA (EVF) by carrying out the following steps: (i) We prepared soaking solutions containing 1.32 M sodium citrate, 1 mM ZnSO4, 100 mM Tris-HCl (pH 7.8), and 5 mM ligand. (ii) We combined 4 uL of soaking solution and 1-2 crystals of HCAII within a drop on the surface of a reservoir cover (EasyXtal CrystalSupport, Qiagen). (iii) To a clear plastic reservoir in a 15-reservoir plate (EasyXtal, Qiagen), we added 1 mL of soaking solution (without ligand present). We attached the reservoir cover to the reservoir and left the entire setup at 4 deg C for 1 week.
Matthews coefficient: 2.12
Solvent content (%): 42.07
Ligand: 1,3-benzothiazole-2-sulfonamide (EVF)
Ligand formula: C7 H6 N2 O2 S2
Ligand molecular weight: 214.265
Ligand SMILES: c1ccc2c(c1)nc(s2)S(=O)(=O)N
Ligand InChI: InChI=1S/C7H6N2O2S2/c8-13(10,11)7-9-5-3-1-2-4-6(5)12-7/h1-4H,(H2,8,10,11)
Release date: 2017-01-11
Notum Inhibitor ARUK3006562 (PDB entry 8BSR)
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): 1.45
R work: 0.1992
R free: 0.2061
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.2
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.94
Solvent content (%): 36.64
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: 2022-12-14
PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with DF852 (PDB entry 5QXS)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYRTVIKEPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62
R work: 0.1735
R free: 0.1963
Average B factor: 31.562
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 1.6M Ammonium Sulfate, 0.1M bis-tris pH 5.5
Matthews coefficient: 4.21
Solvent content (%): 70.75
Ligand: (4aR,7aR,9R)-3,4,7,7a,8,9-hexahydro-4a,9-epoxypyrrolo[3',4':4,5]cyclohepta[1,2-d]imidazole-6(5H)-carbaldehyde (RJ4)
Ligand formula: C11 H13 N3 O2
Ligand molecular weight: 219.24
Ligand SMILES: c1[nH]c2c(n1)C3CC4CN(CC4(C2)O3)C=O
Ligand InChI: InChI=1S/C11H13N3O2/c15-6-14-3-7-1-9-10-8(12-5-13-10)2-11(7,4-14)16-9/h5-7,9H,1-4H2,(H,12,13)/t7-,9-,11+/m1/s1
Release date: 2020-04-08
Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 1 (PDB entry 8OG6)
Macromolecule: DDB1- and CUL4-associated factor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 367 residues
Sequence: GGGREPKQRRQAPINFTSRLNRRASFPKYGGVDGGCFDRHLIFSRFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSALAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVGRQRLAEDEDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.245
R work: 0.2027
R free: 0.2308
Average B factor: 47.665
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris pH 7.0, 2.13M Lithium acetate
Matthews coefficient: 2.78
Solvent content (%): 55.73
Ligand: 5-(2-fluorophenyl)-2,3-dihydroimidazo[2,1-a]isoquinoline (LQH)
Ligand formula: C17 H13 F N2
Ligand molecular weight: 264.297
Ligand SMILES: c1ccc2c(c1)C=C(N3C2=NCC3)c4ccccc4F
Ligand InChI: InChI=1S/C17H13FN2/c18-15-8-4-3-7-14(15)16-11-12-5-1-2-6-13(12)17-19-9-10-20(16)17/h1-8,11H,9-10H2
Release date: 2023-06-14
Human MST3 (STK24) kinase in complex with inhibitor MRLW5 (PDB entry 8BZJ)
Macromolecule: Serine/threonine-protein kinase 24
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 306 residues
Sequence: MRAQLWGLALNKRRATLPHPGGSTNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHSEKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKVLFLIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.182073055088
R free: 0.250313678016
Average B factor: 57.9240676092
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Protein solution: 11 mg/mL MST3 in 25 mM HEPES pH 7.5, 200 mM NaCl, 0.5 mM TCEP, 5% glycerol, with 1 mM inhibitor).
Crystallization buffer: 12% PEG 6000, 0.1 M HEPES pH 7.4.
Matthews coefficient: 2.51
Solvent content (%): 51
Ligand: 8-(4-azanylbutyl)-6-[2-chloranyl-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7-one (SJX)
Ligand formula: C24 H25 Cl N6 O
Ligand molecular weight: 448.948
Ligand SMILES: Cc1cccc(n1)c2ccc(c(c2)Cl)C3=Cc4cnc(nc4N(C3=O)CCCCN)NC
Ligand InChI: InChI=1S/C24H25ClN6O/c1-15-6-5-7-21(29-15)16-8-9-18(20(25)13-16)19-12-17-14-28-24(27-2)30-22(17)31(23(19)32)11-4-3-10-26/h5-9,12-14H,3-4,10-11,26H2,1-2H3,(H,27,28,30)
Release date: 2023-01-18
Crystal structure of DYRK1A in complex with gossypin (PDB entry 8C3R)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 370 residues
Sequence: DSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADEGTNTHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.1855
R free: 0.2091
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5, 0.2 M ammonium acetate, 25% PEG3350
Matthews coefficient: 2.64
Solvent content (%): 53.41
Ligand: Gossypin (R7O)
Ligand formula: C21 H20 O13
Ligand molecular weight: 480.376
Ligand SMILES: c1cc(c(cc1C2=C(C(=O)c3c(cc(c(c3O2)OC4C(C(C(C(O4)CO)O)O)O)O)O)O)O)O
Ligand InChI: InChI=1S/C21H20O13/c22-5-11-13(27)15(29)17(31)21(32-11)34-19-10(26)4-9(25)12-14(28)16(30)18(33-20(12)19)6-1-2-7(23)8(24)3-6/h1-4,11,13,15,17,21-27,29-31H,5H2/t11-,13-,15+,17-,21+/m1/s1
Release date: 2024-01-10
Ni- Carbonic Anhydrase II pH 7.8 20 atm CO2 (PDB entry 6LV6)
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): 1.2
R work: 0.1124
R free: 0.138
Average B factor: 11.027
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.1
Solvent content (%): 41.29
Ligand: CARBON DIOXIDE (CO2)
Ligand formula: C O2
Ligand molecular weight: 44.01
Ligand SMILES: C(=O)=O
Ligand InChI: InChI=1S/CO2/c2-1-3
Release date: 2020-08-19
Crystal structure of SOS1-HRas-peptidomimetic4 (PDB entry 8BE8)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 186 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2069
R free: 0.2369
Average B factor: 58.43
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: sodium formate 3 M, Tris 100mM pH 8.0
Matthews coefficient: 3.54
Solvent content (%): 65.26
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2023-04-26
Calpain-5 (CAPN5) Protease Core (PC) (PDB entry 6P3Q)
Macromolecule: Calpain-5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22
Sequence length: 359 residues
Sequence: GSHMFSCVKPYEDQNYSALRRDCRRRKVLFEDPLFPATDDSLYYKGTPGPAVRWKRPKGICEDPRLFVDGISSHDLHQGQVGNCWFVAACSSLASRESLWQKVIPDWKEQEWDPEKPNAYAGIFHFHFWRFGEWVDVVIDDRLPTVNNQLIYCHSNSRNEFWCALVEKAYAKLAGCYQALDGGNTADALVDFTGGVSEPIDLTEGDFANDETKRNQLFERMLKVHSRGGLISASIKAVTAADMEARLACGLVKGHAYAVTDVRKVRLGHGLLAFFKSEKLDMIRLRNPWGEREWNGPWSDTSEEWQKVSKSEREKMGVTVQDDGEFWMTFEDVCRYFTDIIKCRVILENLYFQGHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2268
R free: 0.2851
Average B factor: 50.18
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 250 mM sodium phosphate, 12 % PEG 8000, 36 mM EDTA, 10 mM Calcium chloride, 0.4 mM H-E(EDANS)-KIEIVRKKPIFKKATV-K(DASBCYL)-OH
Matthews coefficient: 2.71
Solvent content (%): 54.68
Release date: 2020-02-05
Crystal structure of Angiotensin-1 converting enzyme C-domain in complex with fosinoprilat (PDB entry 7Z70)
Macromolecule: Angiotensin-converting enzyme
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1
Sequence length: 597 residues
Sequence: LVTDEAEASKFVEEYDRTSQVVWNEYAGANWNYNTNITTETSKILLQKNMQIAQHTLKYGTQARKFDVNQLQNTTIKRIIKKVQDLERAALPAQELEEYNKILLDMETTYSVATVCHPQGSCLQLEPDLTNVMATSRKYEDLLWAWEGWRDKAGRAILQFYPKYVELINQAARLNGYVDAGDSWRSMYETPSLEQDLERLFQELQPLYLNLHAYVRRALHRHYGAQHINLEGPIPAHLLGNMWAQTWSNIYDLVVPFPSAPSMDTTEAMLKQGWTPRRMFKEADDFFTSLGLLPVPPEFWQKSMLEKPTDGREVVCHASAWDFYNGKDFRIKQCTTVNLEDLVVAHHEMGHIQYFMQYKDLPVALREGANPGFHEAIGDVLALSVSTPKHLHSLNLLSSEGGSDEHDINFLMKMALDKIAFIPFSYLVDQWRWRVFDGSITKENYNQEWWSLRLKYQGLCPPVPRTQGDFDPGAKFHIPSSVPYIRYFVSFIIQFQFHEALCQAAGHTGPLHKCDIYQSKEAGQRLATAMKLGFSRPWPEAMQLITGQPQMSASAMLSYFKPLLDWLRTENELHGEKLGWPQYNWTPNSARSEGPLP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1736
R free: 0.2134
Average B factor: 26.35
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4
Crystallization temperature (K): 289
Crystal growth procedure: 0.1 M MIB pH 4.0, 5% glycerol, 15% PEG 3350
Matthews coefficient: 2.38
Solvent content (%): 48.27
Ligand: fosinoprilat (KS8)
Ligand formula: C23 H34 N O5 P
Ligand molecular weight: 435.494
Ligand SMILES: c1ccc(cc1)CCCCP(=O)(CC(=O)N2CC(CC2C(=O)O)C3CCCCC3)O
Ligand InChI: InChI=1S/C23H34NO5P/c25-22(17-30(28,29)14-8-7-11-18-9-3-1-4-10-18)24-16-20(15-21(24)23(26)27)19-12-5-2-6-13-19/h1,3-4,9-10,19-21H,2,5-8,11-17H2,(H,26,27)(H,28,29)/t20-,21+/m1/s1
Release date: 2022-06-22
Design and Synthesis of a pan-JAK Kinase Inhibitor Clinical Candidate (PF-06263276) Suitable for Inhaled and Topical Delivery for the Treatment of Inflammatory Diseases of the Lungs and Skin (PDB entry 5TQ7)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 304 residues
Sequence: MGHHHHHHEDRDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQSIVTHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQVRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2258
R free: 0.28575
Average B factor: 25.78
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Hepes, pH 7.5, 100 mM sodium acetate, 30% PEG3350
Matthews coefficient: 2.35
Solvent content (%): 47.6
Ligand: {(3R,4R)-4-methyl-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}[(3R)-3-(phenylsulfonyl)pyrrolidin-1-yl]methanone (7GT)
Ligand formula: C24 H30 N6 O3 S
Ligand molecular weight: 482.598
Ligand SMILES: CC1CCN(CC1N(C)c2c3cc[nH]c3ncn2)C(=O)N4CCC(C4)S(=O)(=O)c5ccccc5
Ligand InChI: InChI=1S/C24H30N6O3S/c1-17-9-12-30(15-21(17)28(2)23-20-8-11-25-22(20)26-16-27-23)24(31)29-13-10-19(14-29)34(32,33)18-6-4-3-5-7-18/h3-8,11,16-17,19,21H,9-10,12-15H2,1-2H3,(H,25,26,27)/t17-,19-,21+/m1/s1
Release date: 2017-01-11
Human APE1 product complex (PDB entry 5DFF)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.99.18
Sequence length: 276 residues
Sequence: ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1869
R free: 0.2113
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Matthews coefficient: 2.61
Solvent content (%): 52.82
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: 2015-10-14