satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of human dihydroorotate dehydrogenase in complex with 277-9-OH (PDB entry 5ZF7)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 390 residues
Sequence: MGHHHHHHHHHHSSGHIDDDDKHMATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1623
R free: 0.18043
Average B factor: 24.007
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.9
Crystallization temperature (K): 293
Crystal growth procedure: 100MM SODIUM ACETATE, 1.8-1.9M AMMONIUM SULPHATE, 40MM C11DAO, 20.8MM DDAO, 2MM DIHYDROOROTATE
Matthews coefficient: 3.41
Solvent content (%): 63.92
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2018-09-26
Histone deacetylases complex with peptide macrocycles (PDB entry 6WHN)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 385 residues
Sequence: AAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.54
R work: 0.1628
R free: 0.1924
Average B factor: 24.19
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 40% (v/v) PEG600 and 100mM CHES 
pH 9.5
Matthews coefficient: 2.46
Solvent content (%): 50.07
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: 2021-04-21
Crystal structure of human dihydroorotate dehydrogenase (DHODH) with Piperine (PDB entry 6LZL)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 365 residues
Sequence: TGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1851
R free: 0.2093
Average B factor: 30.005
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.8
Crystallization temperature (K): 293
Crystal growth procedure: HEPES pH 7.7, NaCl, 20% Glycerol, EDTA, UDAO, DDAO
Matthews coefficient: 3.63
Solvent content (%): 66.14
Ligand: OROTIC ACID (ORO)
Ligand formula: C5 H4 N2 O4
Ligand molecular weight: 156.096
Ligand SMILES: C1=C(NC(=O)NC1=O)C(=O)O
Ligand InChI: InChI=1S/C5H4N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h1H,(H,9,10)(H2,6,7,8,11)
Release date: 2020-04-15
Crystal Structure of the Human CAMKK1A in complex with GSK650394 (PDB entry 6CD6)
Macromolecule: Calcium/calmodulin-dependent protein kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 290 residues
Sequence: SMQLNQYKLQSEIGKGAYGVVRLAYNESEDRHYAMKVLSKKKLLKQYGFPRRPPPRGSQAAQGGPAKQLLPLERVYQEIAILKKLDHVNVVKLIEVLDDPAEDNLYLVFDLLRKGPVMEVPCDKPFSEEQARLYLRDVILGLEYLHCQKIVHRDIKPSNLLLGDDGHVKIADFGVSNQFEGNDAQLSSTAGTPAFMAPEAISDSGQSFSGKALDVWATGVTLYCFVYGKCPFIDDFILALHRKIKNEPVVFPEEPEISEELKDLILKMLDKNPETRIGVPDIKLHPWVTK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.23213
R free: 0.2849
Average B factor: 59.267
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 280
Crystal growth procedure: 33.75% PEG2000 MME, 0.15 M potassium thiocyanate, 0.1 M CHC buffer, pH 7.0, cryoprotectant: 30% polyethylene glycol
Matthews coefficient: 2.3
Solvent content (%): 46.55
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: 2018-03-07
Re-refined crystal structure of di-phosphorylated human CLK1 in complex with a novel substituted indole inhibitor (PDB entry 6TW2)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 339 residues
Sequence: SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1806
R free: 0.2225
Average B factor: 35.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 2.1 M SODIUM MALATE
Matthews coefficient: 2.55
Solvent content (%): 51.78
Ligand: ethyl 3-[(E)-2-amino-1-cyanoethenyl]-6,7-dichloro-1-methyl-1H-indole-2-carboxylate (V25)
Ligand formula: C15 H13 Cl2 N3 O2
Ligand molecular weight: 338.189
Ligand SMILES: CCOC(=O)c1c(c2ccc(c(c2n1C)Cl)Cl)C(=CN)C#N
Ligand InChI: InChI=1S/C15H13Cl2N3O2/c1-3-22-15(21)14-11(8(6-18)7-19)9-4-5-10(16)12(17)13(9)20(14)2/h4-6H,3,18H2,1-2H3/b8-6-
Release date: 2020-02-05
syk in complex with 57262_SYKB-AZ13344324-2 (PDB entry 6ZCU)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 299 residues
Sequence: MDTEVYESPYADPEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.188
R free: 0.218
Average B factor: 34.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Na3Cit pH 6.4, 16% PEG3350, 0.2M KH2PO4
Matthews coefficient: 2.06
Solvent content (%): 40.22
Ligand: 6-chloro-2-(2-fluoro-4,5-dimethoxyphenyl)-N-(piperidin-4-ylmethyl)-3H-imidazo[4,5-b]pyridin-7-amine (5JG)
Ligand formula: C20 H23 Cl F N5 O2
Ligand molecular weight: 419.88
Ligand SMILES: COc1cc(c(cc1OC)F)c2[nH]c3c(n2)c(c(cn3)Cl)NCC4CCNCC4
Ligand InChI: InChI=1S/C20H23ClFN5O2/c1-28-15-7-12(14(22)8-16(15)29-2)19-26-18-17(13(21)10-25-20(18)27-19)24-9-11-3-5-23-6-4-11/h7-8,10-11,23H,3-6,9H2,1-2H3,(H2,24,25,26,27)
Release date: 2021-06-23
TEV Cleaved Human ATP Citrate Lyase Bound to Citrate (PDB entry 5TDE)
Macromolecule: ATP-citrate synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.3.8
Sequence length: 431 residues
Sequence: MSAKAISEQTGKELLYKFICTTSAIQNRFKYARVTPDTDWARLLQDHPWLLSQNLVVKPDQLIKRRGKLGLVGVNLTLDGVKSWLKPRLGQEATVGKATGFLKNFLIEPFVPHSQAEEFYVCIYATREGDYVLFHHEGGVDVGDVDAKAQKLLVGVDEKLNPEDIKKHLLVHAPEDKKEILASFISGLFNFYEDLYFTYLEINPLVVTKDGVYVLDLAAKVDATADYICKVKWGDIEFPPPFGREAYPEEAYIADLDAKSGASLKLTLLNPKGRIWTMVAGGGASVVYSDTICDLGGVNELANYGEYSGAPSEQQTYDYAKTILSLMTREKHPDGKILIIGGSIANFTNVAATFKGIVRAIRDYQGPLKEHEVTIFVRRGGPNYQEGLRVMGEVGKTTGIPIHVFGTETHMTAIVGMALGHRPIPENLYFQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1551
R free: 0.1842
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 294
Crystal growth procedure: 12.5% P3350, 100 mM Tris-HCL pH 7.0, 125 mM ammonium phosphate pH 7.5
Matthews coefficient: 2.75
Solvent content (%): 55.25
Ligand: DIHYDROGENPHOSPHATE ION (2HP)
Ligand formula: H2 O4 P
Ligand molecular weight: 96.987
Ligand SMILES: OP(=O)(O)[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-1
Release date: 2017-08-09
Crystal Structure of human phosphodiesterase 10 in complex with ethyl N-[[4-[[4-(azetidine-1-carbonyl)-2-methylpyrazole-3-carbonyl]amino]-6-methylpyridin-2-yl]carbamothioyl]carbamate (PDB entry 5SJP)
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): 2.25
R work: 0.1733
R free: 0.2344
Average B factor: 48.057
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 (%): 53.1
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 uPA in complex with upain-2-4-W3A (PDB entry 5WXR)
Macromolecule: Urokinase-type plasminogen activator chain B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 253 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKEENGLAL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.194
R free: 0.234
Average B factor: 21.6
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 50mM sodium citrate, pH 4.6, 2.0M ammonium sulfate supplemented with 5% polyethylene glycol 400
Matthews coefficient: 2.09
Solvent content (%): 41.04
Release date: 2018-07-11
Crystal structure of Angiotensin-1 converting enzyme C-domain in complex with dual ACE/NEP inhibitor AD011 (PDB entry 7Q27)
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): 1.5
R work: 0.1485
R free: 0.1781
Average B factor: 19.68
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, 16% PEG 3350
Matthews coefficient: 2.35
Solvent content (%): 47.69
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: 2022-02-16
APE1 exonuclease substrate complex with a C/G match (PDB entry 5WN0)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 276 residues
Sequence: ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2169
R free: 0.2749
Average B factor: 46.33
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Matthews coefficient: 2.6
Solvent content (%): 52.7
Release date: 2018-02-28
Extended structure of the human DDX6 C-terminal domain in complex with an EDC3 FDF peptide (PDB entry 6S8S)
Macromolecule: Probable ATP-dependent RNA helicase DDX6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 193 residues
Sequence: GPQDPYEINLMEELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLITYDDRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEYHSEPVEDEKP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.179
R free: 0.226
Average B factor: 40.05
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M CAPS pH 10.5, 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.2 M Li2SO4
Matthews coefficient: 2.8
Solvent content (%): 56.03
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: 2019-09-04
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000514a (PDB entry 5QE4)
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): 1.852
R work: 0.1857
R free: 0.2161
Average B factor: 43.1577
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 (%): 63.22
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2018-10-10
crystal structure of human carbonic anhydrase I in complex with 4-(3-(2-((2-fluorobenzyl)amino)ethyl)ureido) benzenesulfonamide (PDB entry 6XZY)
Macromolecule: Carbonic anhydrase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 261 residues
Sequence: MASPDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.1855
R free: 0.2209
Average B factor: 28.38
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 200 mM Na-acetate, 30% PEG 4000, 100 mM Tris-HCl pH 9.
Inhibitor: 150 mM NaCl, 10% DMSO,  50 mM Tris pH 7
Matthews coefficient: 2.32
Solvent content (%): 47.09
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: 2020-09-23
Crystal Structure of NatD bound to H4/H2A peptide and CoA (PDB entry 4U9W)
Macromolecule: N-alpha-acetyltransferase 40
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1
Sequence length: 207 residues
Sequence: GSMEERAAMDAVCAKVDAANRLGDPLEAFPVFKKYDRNGLNVSIECKRVSGLEPATVDWAFDLTKTNMQTMYEQSEWGWKDREKREEMTDDRAWYLIAWENSSVPVAFSHFRFDVECGDEVLYCYEVQLESKVRRKGLGKFLIQILQLMANSTQMKKVMLTVFKHNHGAYQFFREALQFEIDDSSPSMSGCCGEDCSYEILSRRTKF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.49
R work: 0.176
R free: 0.223
Average B factor: 26.59
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 3350, 200 mM sodium malonate
Matthews coefficient: 2.44
Solvent content (%): 49.51
Ligand: COENZYME A (COA)
Ligand formula: C21 H36 N7 O16 P3 S
Ligand molecular weight: 767.534
Ligand SMILES: CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O
Ligand InChI: InChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
Release date: 2015-01-28
Binary product complex crystal structure of DNA polymerase Beta with an extra-helical template base (PDB entry 6PH5)
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): 2.602
R work: 0.2052
R free: 0.2787
Average B factor: 51.9991
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.41
Solvent content (%): 48.97
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2019-12-11
PKG I's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with PET-cGMP (PDB entry 5JD7)
Macromolecule: cGMP-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.12
Sequence length: 135 residues
Sequence: GSTGLIKHTEYMEFLKSVPTFQSLPEEILSKLADVLEETHYENGEYIIRQGARGDTFFIISKGTVNVTREDSPSEDPVFLRTLGKGDWFGEKALQGEDVRTANVIAAEAVTCLVIDRDSFKHLIGGLDDVSNKAY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.749
R work: 0.1934
R free: 0.2265
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 30% PEG 400, 200 mM CaAc, 0.1M NaAc pH 4.5-4.8.
Matthews coefficient: 1.72
Solvent content (%): 32.83
Ligand: 3-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxotetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-6-phenyl-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one (6JR)
Ligand formula: C18 H16 N5 O7 P
Ligand molecular weight: 445.323
Ligand SMILES: c1ccc(cc1)c2cn3c(n2)Nc4c(ncn4C5C(C6C(O5)COP(=O)(O6)O)O)C3=O
Ligand InChI: InChI=1S/C18H16N5O7P/c24-13-14-11(7-28-31(26,27)30-14)29-17(13)23-8-19-12-15(23)21-18-20-10(6-22(18)16(12)25)9-4-2-1-3-5-9/h1-6,8,11,13-14,17,24H,7H2,(H,20,21)(H,26,27)/t11-,13-,14-,17-/m1/s1
Release date: 2017-08-09
Crystal Structure of Anaplastic Lyphoma Kinase (ALK) in complex with 4 (PDB entry 5IUI)
Macromolecule: ALK tyrosine kinase receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 327 residues
Sequence: RTSTIMTDYNPNYSFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVEEEEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.1794
R free: 0.2051
Average B factor: 30.3485
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.6
Crystallization temperature (K): 277
Crystal growth procedure: 18% PEG 2000 MME, 0.1M Tris-HCl pH 8.6
Matthews coefficient: 2.12
Solvent content (%): 42.05
Ligand: N-[3-(4-amino-3-methylphenyl)-1H-pyrazol-5-yl]-4-[(4-methylpiperazin-1-yl)methyl]benzamide (45Q)
Ligand formula: C23 H28 N6 O
Ligand molecular weight: 404.508
Ligand SMILES: Cc1cc(ccc1N)c2cc([nH]n2)NC(=O)c3ccc(cc3)CN4CCN(CC4)C
Ligand InChI: InChI=1S/C23H28N6O/c1-16-13-19(7-8-20(16)24)21-14-22(27-26-21)25-23(30)18-5-3-17(4-6-18)15-29-11-9-28(2)10-12-29/h3-8,13-14H,9-12,15,24H2,1-2H3,(H2,25,26,27,30)
Release date: 2016-05-18
Crystal structure apo CDK2/cyclin A (PDB entry 5IF1)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.61
R work: 0.18743
R free: 0.23632
Average B factor: 60.552
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277.15
Crystal growth procedure: 100mM HEPES, 5mM DTT, 0.5 mM Kcl, 875mM ammonium sulfate
Matthews coefficient: 4.15
Solvent content (%): 70.33
Release date: 2016-04-27