satarupa22/MacromolecularLigandDB huggingface dataset:
Cytochrome P450 3A4 bound to an inhibitor (PDB entry 4D78)
Macromolecule: CYTOCHROME P450 3A4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.13.157
Sequence length: 487 residues
Sequence: MAYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDGTVSGAHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.19295
R free: 0.27237
Average B factor: 102.012
Crystallization method: MICROBATCH
Crystallization pH: 5
Crystal growth procedure: MICROBATCH UNDER OIL WITH 10% PEG 3350 AND 80 MM SODIUM MALONATE PH 5.0
Matthews coefficient: 2.38
Solvent content (%): 48.3
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: 2015-09-23
Ternary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dA (PDB entry 8VFI)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACGACGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.1806
R free: 0.2287
Average B factor: 26.24
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: 2.31
Solvent content (%): 46.7
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: 2024-05-15
Crystal Structure of p38alpha in Complex with Lipid Pocket Ligand 9j (PDB entry 5N66)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2062
R free: 0.2377
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM MES pH 5.6-6.2
20-30 % PEG4000
50 mM BOG
Matthews coefficient: 2.39
Solvent content (%): 48.48
Ligand: ~{N}4-[[4-(cyclopropylmethyl)furan-2-yl]methyl]-2-phenyl-quinazoline-4,7-diamine (BW1)
Ligand formula: C23 H22 N4 O
Ligand molecular weight: 370.447
Ligand SMILES: c1ccc(cc1)c2nc3cc(ccc3c(n2)NCc4cc(co4)CC5CC5)N
Ligand InChI: InChI=1S/C23H22N4O/c24-18-8-9-20-21(12-18)26-22(17-4-2-1-3-5-17)27-23(20)25-13-19-11-16(14-28-19)10-15-6-7-15/h1-5,8-9,11-12,14-15H,6-7,10,13,24H2,(H,25,26,27)
Release date: 2017-09-20
COMPLEMENT FACTOR D IN COMPLEX WITH A REVERSIBLE INDOLE CARBOXYLIC ACID BASED INHIBITOR (PDB entry 5MT0)
Macromolecule: Complement factor D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.46
Sequence length: 232 residues
Sequence: ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLASAAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.154
R free: 0.196
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG3350, 100 mM BIS-TRIS pH 6.5
Matthews coefficient: 2.09
Solvent content (%): 41.21
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: 2017-02-15
SETDB1 in complex with a fragment candidate (PDB entry 5KH6)
Macromolecule: Histone-lysine N-methyltransferase SETDB1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 211 residues
Sequence: ENLYFQGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYDYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.178
R free: 0.235
Average B factor: 32.94
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 25% PEG-3350, 0.2M lithium sulfate, 0.1M bis-tris. Trypsin had been added to the protein stock solution.
Matthews coefficient: 2.54
Solvent content (%): 51.57
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: 2016-09-21
Structure of cyclophilin A in complex with 2-chloropyridin-3-amine (PDB entry 5NOX)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.16856
R free: 0.19876
Average B factor: 19.623
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 279.15
Crystal growth procedure: PEG 8000, Tris-HCl
Matthews coefficient: 2.82
Solvent content (%): 56.43
Ligand: 2-chloranylpyridin-3-amine (L97)
Ligand formula: C5 H5 Cl N2
Ligand molecular weight: 128.56
Ligand SMILES: c1cc(c(nc1)Cl)N
Ligand InChI: InChI=1S/C5H5ClN2/c6-5-4(7)2-1-3-8-5/h1-3H,7H2
Release date: 2017-07-12
HRAS R97L Crystal Form 2 (PDB entry 8FG3)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 166 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYLEQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.206
R free: 0.2473
Average B factor: 21.13
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: PEG 3350,
Calcium Acetate,
Magnesium Chloride,
Sodium Chloride,
DTT
Matthews coefficient: 1.91
Solvent content (%): 35.61
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2023-09-06
Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT (PDB entry 7RJL)
Macromolecule: Bromodomain-containing protein 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 123 residues
Sequence: SMPEVSNPSKPGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQEE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1571
R free: 0.1847
Average B factor: 26.065
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 292
Crystal growth procedure: 35% v/v Tacsimate
Matthews coefficient: 2.16
Solvent content (%): 43.12
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: 2022-08-03
Structural mechanism of Nek7 activation by Nek9-induced dimerisation (PDB entry 5DE2)
Macromolecule: Serine/threonine-protein kinase Nek7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 310 residues
Sequence: MDEQSQGMQGPPVPQFQPQKALRPDMGYNTLANFRIEKKIGRGQFSEVYRAACLLDGVPVALKKVQIFDLMDAKARADCIKEIDLLKQLNHPNVIKFYASFIEDNELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALEHMHSRRVMHRDIKPANVFITATGVVKLGDLGLGRFFSSKTTAAHSLVGTPYYMSPERIHENGYNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNMCINPDPEKRPDVTYVYDVAKRMHACTASSLEHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.78
R work: 0.2059
R free: 0.2535
Average B factor: 66.35
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: The composition of the reservoir buffer was: 0.2M Potassium thiocyanate, 0.1M Bis-Tris propane pH 7.5, 20% (w/v) PEG 3350.
Matthews coefficient: 2.3
Solvent content (%): 46.56
Release date: 2015-11-11
DDR1, 3-chloro-N-[(1R,2S)-2-phenylcyclopropyl]-5-(1H-pyrrolo[2,3-b]pyridin-5-yloxymethyl)benzamide, 1.600A, P212121, Rfree=23.2% (PDB entry 5SB2)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 321 residues
Sequence: PGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.2074
R free: 0.232
Average B factor: 35.8779
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 11.5 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed with reservoir consisting of 0.1M MES/NaOH pH 6.5, 0.2M KI, 25% PEG 4000
Matthews coefficient: 2.17
Solvent content (%): 43.34
Ligand: IODIDE ION (IOD)
Ligand formula: I
Ligand molecular weight: 126.904
Ligand SMILES: [I-]
Ligand InChI: InChI=1S/HI/h1H/p-1
Release date: 2022-06-29
Human endoplasmic reticulum aminopeptidase 1 (ERAP1) in complex with (4aR,5S,6R,8S,8aR)-5-(2-(Furan-3-yl)ethyl)-8-hydroxy-5,6,8a-trimethyl-3,4,4a,5,6,7,8,8a-octahydronaphthalene-1-carboxylic acid (PDB entry 6T6R)
Macromolecule: Endoplasmic reticulum aminopeptidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11
Sequence length: 922 residues
Sequence: MVFLPLKWSLATMSFLLSSLLALLTVSTPSWCQSTEASPKRSDGTPFPWNKIRLPEYVIPVHYDLLIHAQLTTLTFWGTTKVEITASQPTSTIILHSHHLQISRATLRKGAGERLSEEPLQVLEHPRQEQIALLAPEPLLVGLPYTVVIHYAGQLSETFHGFYKSTYRTKEGELRILASTQFEPTAARMAFPCFDEPAFKASFSIKIRREPRHLAISNMPLVKSVTVAEGLIEDHFDVTVKMSTYLVAFIISDFESVSKITKSGVKVSVYAVPDKINQADYALDAAVTLLEFYEDYFSIPYPLPKQDLAAIPDFQSGAMENWGLTTYRESALLFDAEKSSASSKLGITMTVAHELAHQWFGNLVTMEWWNDLWLNEGFAKFMEFVSVSVTHPELKVGDYFFGKCFDAMEVDALQSSHPVSTPVENPAQIREMFDDVSYDKGACILNMLREYLSADAFKSGIVQYLQKHSYKNTKNEDLWDSMASIGSGGVDVKTMMNTWTLQKGFPLITITVRGRNVHMKQEHYMKGSDGAPDTGYLWHVPLTFITSKSDMVHRFLLKTKTDVLILPEEVEWIKFNVGMNGYYIVHYEDDGWDSLTGLLKGTHTAVSSNDRASLINNAFQLVSIGKLSIEKALDLSLYLKHETEIMPVFQGLNELIPMYKLMEKRDMNEVETQFKAFLIRLLRDLIDKQTWTDEGSVSERMLRSQLLLLACVHNYQPCVQRAEGYFRKWKESNGQLSLPVDVTLAVFAVGAQSTEGWDFLYSKYQFSLSSTEKSQIEFALCRTQNKEKLQWLLDESFKGDKIKTQEFPQILTLIGRNPVGYPLAWQFLRKNWNKLVQKFELGSSSIAHMVMGTTNQFSTRTRLEEVKGFFSSLKENGSQLRCVQQTIETIEENIGWMDKNFDKIRVWLQSEKLERMENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.169
R free: 0.194
Average B factor: 31.03
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 293
Crystal growth procedure: PACT condition D1 (0.1M MMT, pH 4.0, 25% PEG 1500), MMT = DL-malic acid, MES monohydrate, Tris
Matthews coefficient: 2.18
Solvent content (%): 43.65
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: 2020-03-18
Crystal structure of human MTH1(G2K/D120N mutant) in complex with 8-oxo-dGTP at pH 7.0 (PDB entry 5GHM)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 156 residues
Sequence: MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDNSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.173
R free: 0.1961
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: Sodium citrate, Tris, NaCl
Matthews coefficient: 1.87
Solvent content (%): 34.35
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-01-04
Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5) (PDB entry 7NPI)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase MINDY-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 273 residues
Sequence: GPLGSPEFMSVYHIKWIQWKEENTPIITQNENGPAPLLAILNVLLLAWKVKLPPMMEIITAEQLMEYLGDYMLDAKPKEISEIQRLNYEQNMSDAMAILHKLQTGLDVNVRFTGVRVFEYTPECIVFDLLDIPLYHGWLVDPQIDDIVKAVGNCSYNQLVEKIISCKQSDNSELVSEGFVAEQFLNNTATQLTYHGLCELTSTVQEGELCVFFRNNHFSTMTKYKGQLYLLVTDQGFLTEEKVVWESLHNVDGDGNFCDSEFHLRPPSDPETV
Oligomeric state: Hetero 6-mer
Stoichiometry: A5, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.81
R work: 0.2284
R free: 0.2877
Average B factor: 68.21
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 3% w/v Dextran sulphate sodium salt
0.1 M BICINE pH 8.5
15% w/v PEG 20,000
Matthews coefficient: 4.02
Solvent content (%): 69.4
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2021-09-15
Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues (PDB entry 5AQF)
Macromolecule: HEAT SHOCK COGNATE 71 KDA PROTEIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.51
Sequence length: 386 residues
Sequence: GPLGSMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.1695
R free: 0.2076
Average B factor: 34.95
Crystallization pH: 8.5
Crystal growth procedure: HSC70/BAG1 COMPLEX AT 10 MG/ML INCUBATED WITH 5 MM ADENOSINE, MIXED 1:1 WITH 16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL
Matthews coefficient: 2.5
Solvent content (%): 51
Ligand: ADENOSINE (ADN)
Ligand formula: C10 H13 N5 O4
Ligand molecular weight: 267.241
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N
Ligand InChI: InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
Release date: 2016-10-05
Crystal Structure of human phosphodiesterase 10 in complex with 1-benzyl-3-(2-phenylpyrazol-3-yl)pyridazin-4-one (PDB entry 5SGV)
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
R work: 0.189
R free: 0.2235
Average B factor: 35.025
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: 2.61
Solvent content (%): 52.92
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
Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor (PDB entry 5A0C)
Macromolecule: NEUTROPHIL ELASTASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.37
Sequence length: 218 residues
Sequence: IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.16302
R free: 0.21279
Average B factor: 27.223
Crystal growth procedure: 0.1M MES AT PH6.5,1.2M SODIUMMALONATE
Matthews coefficient: 2.4
Solvent content (%): 48.71
Ligand: (6S)-6-(4-cyano-2-methylsulfonyl-phenyl)-4-methyl-2-oxidanylidene-3-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-5-carbonitrile (JJV)
Ligand formula: C21 H15 F3 N4 O3 S
Ligand molecular weight: 460.429
Ligand SMILES: CC1=C(C(NC(=O)N1c2cccc(c2)C(F)(F)F)c3ccc(cc3S(=O)(=O)C)C#N)C#N
Ligand InChI: InChI=1S/C21H15F3N4O3S/c1-12-17(11-26)19(16-7-6-13(10-25)8-18(16)32(2,30)31)27-20(29)28(12)15-5-3-4-14(9-15)21(22,23)24/h3-9,19H,1-2H3,(H,27,29)/t19-/m1/s1
Release date: 2015-08-19
Crystal structure of the CREBBP bromodomain in complex with a tetrahydroquinoxaline ligand (PDB entry 6YIK)
Macromolecule: CREBBP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.156
R free: 0.184
Average B factor: 32.625
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 21% PEG3350
15% ethylene glycol
0.25M sodium formate
Matthews coefficient: 3.42
Solvent content (%): 64.06
Ligand: (3~{R})-~{N}-[3-(3,4-dihydro-2~{H}-quinolin-1-yl)-2,2-bis(fluoranyl)propyl]-3-methyl-2-oxidanylidene-3,4-dihydro-1~{H}-quinoxaline-5-carboxamide (OSQ)
Ligand formula: C22 H24 F2 N4 O2
Ligand molecular weight: 414.448
Ligand SMILES: CC1C(=O)Nc2cccc(c2N1)C(=O)NCC(CN3CCCc4c3cccc4)(F)F
Ligand InChI: InChI=1S/C22H24F2N4O2/c1-14-20(29)27-17-9-4-8-16(19(17)26-14)21(30)25-12-22(23,24)13-28-11-5-7-15-6-2-3-10-18(15)28/h2-4,6,8-10,14,26H,5,7,11-13H2,1H3,(H,25,30)(H,27,29)/t14-/m1/s1
Release date: 2020-04-15
Crystal Structure of Human Kallikrein 6 in complex with GSK578724A (PDB entry 6QHB)
Macromolecule: Kallikrein-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 223 residues
Sequence: LVHGGPCDKTSHPYQAALYTSGHLLCGGVLIHPLWVLTAAHCKKPNLQVFLGKHNLGQQESSQEQSSVVRAVIHPDYDAASHDQDIMLLRLARPAKLSELIQPLPLERDCSAQTTSCHILGWGKTADGDFPDTIQCAYIHLVSREECEHAYPGQITQNMLCAGDEKYGKDSCQGDSGGPLVCGDHLRGLVSWGNIPCGSKEKPGVYTNVCRYTNWIQKTIQAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.183
R free: 0.206
Average B factor: 30.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.6
Crystallization temperature (K): 293
Crystal growth procedure: 100mM Tris-HCl pH 8.6, PEG 4000 18-28%
Matthews coefficient: 2.46
Solvent content (%): 50.08
Ligand: ~{N}-(4-carbamimidoylphenyl)-3-methoxy-2-oxidanyl-benzamide (J2W)
Ligand formula: C15 H15 N3 O3
Ligand molecular weight: 285.298
Ligand SMILES: COc1cccc(c1O)C(=O)Nc2ccc(cc2)C(=N)N
Ligand InChI: InChI=1S/C15H15N3O3/c1-21-12-4-2-3-11(13(12)19)15(20)18-10-7-5-9(6-8-10)14(16)17/h2-8,19H,1H3,(H3,16,17)(H,18,20)
Release date: 2019-02-06
Crystal structure of MST3 with a pyrrolopyrimidine inhibitor (PF-06454589). (PDB entry 4W8D)
Macromolecule: Serine/threonine-protein kinase 24 36 kDa subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 290 residues
Sequence: GLPGMQNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHSEKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKVLFLIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDRYKRWKAEQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.1711
R free: 0.1824
Average B factor: 37.84
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris-HCL (pH 8.5), 180mM MgCl2, 5mM Manganese acetate, 10-17% PEG 3350
Matthews coefficient: 2.74
Solvent content (%): 55.15
Ligand: 5-(1-methyl-1H-pyrazol-4-yl)-4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidine (3JA)
Ligand formula: C14 H16 N6 O
Ligand molecular weight: 284.316
Ligand SMILES: Cn1cc(cn1)c2c[nH]c3c2c(ncn3)N4CCOCC4
Ligand InChI: InChI=1S/C14H16N6O/c1-19-8-10(6-18-19)11-7-15-13-12(11)14(17-9-16-13)20-2-4-21-5-3-20/h6-9H,2-5H2,1H3,(H,15,16,17)
Release date: 2015-03-18