satarupa22/MacromolecularLigandDB huggingface dataset:
Human DNA polymerase lambda L431A mutant- Apoenzyme and complex with 6 paired DNA (PDB entry 5CP2)
Macromolecule: DNA (5'-D(P*GP*TP*AP*CP*TP*G)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 6 residues
Sequence: GTACTG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.206
R free: 0.238
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Matthews coefficient: 2.57
Solvent content (%): 52.19
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: 2016-02-24
Crystal structure of the catalytic domain of human JARID1B in complex with MC3962 (PDB entry 5FZF)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.1786
R free: 0.2114
Crystallization pH: 7.5
Crystal growth procedure: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC
Matthews coefficient: 2.07
Solvent content (%): 40.67
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: 2017-03-29
Crystal Structure of KRasG13C in Complex with Nucleotide-based covalent Inhibitor bdaGDP (PDB entry 7OK4)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: HMTEYKLVVVGAGCVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1653
R free: 0.1824
Average B factor: 37.3486
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M (NH4)F, 20 % PEG3350, 70 mg/mL KRas-bdaGDP, 0.1 uL reservoir + 0.1 uL protein solution
Matthews coefficient: 2.22
Solvent content (%): 44.66
Ligand: bdaGDP (VJB)
Ligand formula: C18 H29 N7 O13 P2
Ligand molecular weight: 613.409
Ligand SMILES: CCC(=O)NCCCCNC(=O)OC1C(OC(C1O)n2cnc3c2NC(=NC3=O)N)COP(=O)(O)OP(=O)(O)O
Ligand InChI: InChI=1S/C18H29N7O13P2/c1-2-10(26)20-5-3-4-6-21-18(29)37-13-9(7-35-40(33,34)38-39(30,31)32)36-16(12(13)27)25-8-22-11-14(25)23-17(19)24-15(11)28/h8-9,12-13,16,27H,2-7H2,1H3,(H,20,26)(H,21,29)(H,33,34)(H2,30,31,32)(H3,19,23,24,28)/t9-,12-,13-,16-/m1/s1
Release date: 2022-08-03
Crystal structure of DAPK1 in complex with luteolin. (PDB entry 5AUU)
Macromolecule: Death-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 293 residues
Sequence: MTVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1791
R free: 0.2162
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 2 M ammonium sulfate, 0.1 M MES
Matthews coefficient: 1.92
Solvent content (%): 35.81
Ligand: 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one (LU2)
Ligand formula: C15 H10 O6
Ligand molecular weight: 286.236
Ligand SMILES: c1cc(c(cc1C2=CC(=O)c3c(cc(cc3O2)O)O)O)O
Ligand InChI: InChI=1S/C15H10O6/c16-8-4-11(19)15-12(20)6-13(21-14(15)5-8)7-1-2-9(17)10(18)3-7/h1-6,16-19H
Release date: 2015-10-07
Structure of RNF165 in complex with a UbcH5b~Ub conjugate (PDB entry 5ULH)
Macromolecule: Ubiquitin-conjugating enzyme E2 D2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 152 residues
Sequence: GPLGSMALKRIHKELNDLARDPPAQSSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSISSLLSDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1888
R free: 0.2174
Average B factor: 37.942
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 200 mM potassium thiocyanate, 20% PEG 3350
Matthews coefficient: 2.73
Solvent content (%): 54.94
Ligand: THIOCYANATE ION (SCN)
Ligand formula: C N S
Ligand molecular weight: 58.082
Ligand SMILES: C(#N)[S-]
Ligand InChI: InChI=1S/CHNS/c2-1-3/h3H/p-1
Release date: 2017-06-07
Crystal structure of the covalently bonded complex of rilzabrutinib with BTK (PDB entry 7L5P)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 271 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.2237
R free: 0.2582
Average B factor: 27.536
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: PEG 5000 MME AMMONIUM SULFATE MES
Matthews coefficient: 2.44
Solvent content (%): 49.72
Ligand: (2E)-2-{(3R)-3-[4-amino-3-(2-fluoro-4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidine-1-carbonyl}-4-methyl-4-[4-(oxetan-3-yl)piperazin-1-yl]pent-2-enenitrile (R1L)
Ligand formula: C36 H40 F N9 O3
Ligand molecular weight: 665.76
Ligand SMILES: CC(C)(C=C(C#N)C(=O)N1CCCC(C1)n2c3c(c(n2)c4ccc(cc4F)Oc5ccccc5)c(ncn3)N)N6CCN(CC6)C7COC7
Ligand InChI: InChI=1S/C36H40FN9O3/c1-36(2,45-15-13-43(14-16-45)26-21-48-22-26)18-24(19-38)35(47)44-12-6-7-25(20-44)46-34-31(33(39)40-23-41-34)32(42-46)29-11-10-28(17-30(29)37)49-27-8-4-3-5-9-27/h3-5,8-11,17-18,23,25-26H,6-7,12-16,20-22H2,1-2H3,(H2,39,40,41)/b24-18+/t25-/m1/s1
Release date: 2022-06-29
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (R & S isomers, beta, gamma dCTP analogue (PDB entry 6CTT)
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
R work: 0.176
R free: 0.222
Average B factor: 26.56
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.29
Solvent content (%): 46.34
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: 2018-06-20
Crystal Structure of human phosphodiesterase 10 in complex with 2-methyl-4-(morpholine-4-carbonyl)-N-(2-phenylimidazo[1,2-a]pyridin-7-yl)pyrazole-3-carboxamide, space group I23 (PDB entry 5SI1)
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): 1.75
R work: 0.1747
R free: 0.201
Average B factor: 28.304
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: 3.04
Solvent content (%): 59.55
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 EGFR T790M/V948R in Complex with Covalent Pyrrolopyrimidine 19 (PDB entry 6TFZ)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 333 residues
Sequence: GSHMASGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1741
R free: 0.2065
Average B factor: 34.9242
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30 % PEG3350, 100 mM MgSO4, 4 % ethylen glycole 7.5 mg/mL EGFR T790M/V948R (in 100 mM NaCl, 25 mM Tris-HCl, 10 % glycerol, 1 mM TCEP, pH 8.0) 1 ul reservoir + 1 ul protein solution)
Matthews coefficient: 2.31
Solvent content (%): 46.83
Ligand: ~{N}-[2-(2-hydroxyethyloxy)-5-[4-[[1-(phenylmethyl)indazol-5-yl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]phenyl]propanamide (N7B)
Ligand formula: C31 H29 N7 O3
Ligand molecular weight: 547.607
Ligand SMILES: CCC(=O)Nc1cc(ccc1OCCO)c2c[nH]c3c2c(ncn3)Nc4ccc5c(c4)cnn5Cc6ccccc6
Ligand InChI: InChI=1S/C31H29N7O3/c1-2-28(40)37-25-15-21(8-11-27(25)41-13-12-39)24-17-32-30-29(24)31(34-19-33-30)36-23-9-10-26-22(14-23)16-35-38(26)18-20-6-4-3-5-7-20/h3-11,14-17,19,39H,2,12-13,18H2,1H3,(H,37,40)(H2,32,33,34,36)
Release date: 2020-09-30
Crystal structure of DCLK1 Autoinhibited Kinase Domain (PDB entry 6KYQ)
Macromolecule: Serine/threonine-protein kinase DCLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: GSGFQIPATITERYKVGRTIGDGNFAVVKECVERSTAREYALKIIKKSKCRGKEHMIQNEVSILRRVKHPNIVLLIEEMDVPTELYLVMELVKGGDLFDAITSTNKYTERDASGMLYNLASAIKYLHSLNIVHRDIKPENLLVYEHQDGSKSLKLGDFGLATIVDGPLYTVCGTPTYVAPEIIAETGYGLKVDIWAAGVITYILLCGFPPFRGSGDDQEVLFDQILMGQVDFPSPYWDNVSDSAKELITMMLLVDVDQRFSAVQVLEHPWVNDDGLPENEHQLSVAGKIKKHFNTGPKPNSTAAGVSVIATTALDKERQVFRRRRNQD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.141
R work: 0.1606
R free: 0.198
Average B factor: 31.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.6M NaH2PO4, 1.6M K2HPO4, PH7.8
Matthews coefficient: 3.76
Solvent content (%): 67.3
Ligand: BETA-MERCAPTOETHANOL (BME)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: C(CS)O
Ligand InChI: InChI=1S/C2H6OS/c3-1-2-4/h3-4H,1-2H2
Release date: 2020-09-23
Crystal structure of human FAD synthase PAPS domain in complex with FAD (PDB entry 8ROM)
Macromolecule: FAD synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.2
Sequence length: 202 residues
Sequence: GSHMPNAVEQASEAVYKLAESGSSLGKKVAGALQTIETSLAQYSLTQLCVGFNGGKDCTALLHLFHAAVQRKLPDVPNPLQILYIRSISPFPELEQFLQDTIKRYNLQMLEAEGSMKQALGELQARHPQLEAVLMGTRRTDPYSCSLCPFSPTDPGWPAFMRINPLLDWTYRDIWDFLRQLFVPYCILYDRGYTSLGSRENT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1815
R free: 0.2066
Average B factor: 34.06
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M Na/K phosphate, pH 6, 10% DMSO
Matthews coefficient: 2.58
Solvent content (%): 52.4
Ligand: FLAVIN-ADENINE DINUCLEOTIDE (FAD)
Ligand formula: C27 H33 N9 O15 P2
Ligand molecular weight: 785.55
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
Ligand InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
Release date: 2024-04-10
Crystal structure of the EphA2 S897E/S901E mutant intracellular KD-SAM domains (PDB entry 7KJB)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 390 residues
Sequence: GPGDPHTYEDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPETSGEEGVPFRTVSEWLESIKMQQYTEHFMAAGYTAIEKVVQMTNDDIKRIGVRLPGHQKRIAYSLLGLKDQVNTVGIPI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.1976
R free: 0.246
Average B factor: 57.16
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 287
Crystal growth procedure: 4.5% Tacsimate, 0.09 M HEPES pH 7.0, 9% PEG-MME 5K, 0.1 M CsCl
Matthews coefficient: 2.91
Solvent content (%): 57.78
Ligand: CESIUM ION (CS)
Ligand formula: Cs
Ligand molecular weight: 132.905
Ligand SMILES: [Cs+]
Ligand InChI: InChI=1S/Cs/q+1
Release date: 2021-02-03
Crystal structure of the FGFR2 D2 domain in complex with Fab 2B.1.3 (PDB entry 4WV1)
Macromolecule: Fibroblast growth factor receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 99 residues
Sequence: APYWTNTEKMEKRLHAVPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGNYTCVVENEYGSINHTYHLDVVER
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.362
R work: 0.1983
R free: 0.2441
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: PEG 3350, potassium nitrate
Matthews coefficient: 2.52
Solvent content (%): 51.18
Release date: 2015-09-16
Crystal structure of human Sirt2 in complex with a SirReal probe fragment (PDB entry 5DY5)
Macromolecule: NAD-dependent protein deacetylase sirtuin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 304 residues
Sequence: GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.18989
R free: 0.20495
Average B factor: 30.184
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 17.5 % (wt/v) PEG 3350, 0.1 M HEPES
Matthews coefficient: 2.9
Solvent content (%): 57.66
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: 2016-01-20
BACE-2 in complex with ligand 36 (PDB entry 7N4N)
Macromolecule: Beta-secretase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.45
Sequence length: 386 residues
Sequence: ANFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAGTPHSYIDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLVNIATIFESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIPNVFSMQMCGAGLPVAGSGTNGGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFDAVVEAVARASLIPEFSDGFWTGSQLACWTNSETPWSYFPKISIYLRDENSSRSFRITILPQLYIQPMMGAGLNYECYRFGISPSTNALVIGATVMEGFYVIFDRAQKRVGFAASPCAEIAGAAVSEISGPFSTEDVASNCVPA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.163
R free: 0.207
Average B factor: 25.057
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 22.5% PEG-1500, 25 mM Bis-Tris Propane pH 7.0, 150 mM NaCl
Matthews coefficient: 2.32
Solvent content (%): 46.96
Ligand: N-{3-[(2S,5R)-6-amino-2-(fluoromethyl)-5-(methanesulfonyl)-5-methyl-2,3,4,5-tetrahydropyridin-2-yl]-4-fluorophenyl}-6-methoxypyrimidine-4-carboxamide (0BK)
Ligand formula: C20 H23 F2 N5 O4 S
Ligand molecular weight: 467.49
Ligand SMILES: CC1(CCC(N=C1N)(CF)c2cc(ccc2F)NC(=O)c3cc(ncn3)OC)S(=O)(=O)C
Ligand InChI: InChI=1S/C20H23F2N5O4S/c1-19(32(3,29)30)6-7-20(10-21,27-18(19)23)13-8-12(4-5-14(13)22)26-17(28)15-9-16(31-2)25-11-24-15/h4-5,8-9,11H,6-7,10H2,1-3H3,(H2,23,27)(H,26,28)/t19-,20-/m1/s1
Release date: 2021-10-06
Notum-Fragment 151 (PDB entry 7B8D)
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): 1.62
R work: 0.2066
R free: 0.2284
Average B factor: 23.9334
Crystallization method: EVAPORATION
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.98
Solvent content (%): 37.93
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: 2022-01-12
Structure-Based Design of ASK1 Inhibitors as Potential First-in-Class Agents for Heart Failure (PDB entry 5UOR)
Macromolecule: Mitogen-activated protein kinase kinase kinase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 270 residues
Sequence: LLEYDYEYDENGDRVVLGKGTYGIVYAGRDLSNQVRIAIKEIPERDSRYSQPLHEEIALHKHLKHKNIVQYLGSFSENGFIKIFMEQVPGGSLSALLRSKWGPLKDNEQTIGFYTKQILEGLKYLHDNQIVHRDIKGDNVLINTYSGVLKISDFGTSKRLAGINPCTETFTGTLQYMAPEIIDKGPRGYGKAADIWSLGCTIIEMATGKPPFYELGEPQAAMFKVGMFKVHPEIPESMSAEAKAFILKCFEPDPDKRACANDLLVDEFLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2022
R free: 0.2673
Average B factor: 74.263
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 6% polyethylene glycol 2000 MME , 0.1M MES, pH 6.0
Matthews coefficient: 3.16
Solvent content (%): 61.01
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: 2017-06-07
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOOA000540a (PDB entry 5QGA)
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): 1.653
R work: 0.1933
R free: 0.2155
Average B factor: 40.0566
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: 3.31
Solvent content (%): 62.89
Ligand: 2-[(4R)-4-hydroxy-1,1-dioxo-3,4-dihydro-1lambda~6~,2-benzothiazin-2(1H)-yl]acetamide (JQ7)
Ligand formula: C10 H12 N2 O4 S
Ligand molecular weight: 256.278
Ligand SMILES: c1ccc2c(c1)C(CN(S2(=O)=O)CC(=O)N)O
Ligand InChI: InChI=1S/C10H12N2O4S/c11-10(14)6-12-5-8(13)7-3-1-2-4-9(7)17(12,15)16/h1-4,8,13H,5-6H2,(H2,11,14)/t8-/m0/s1
Release date: 2018-10-10
Crystal Structure of human phosphodiesterase 10 in complex with 2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-6-(trifluoromethyl)-[1,2,4]triazolo[1,5-a]pyridine (PDB entry 5SEU)
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): 2.09
R work: 0.1829
R free: 0.238
Average B factor: 45.701
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 (%): 53.09
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: 2022-10-12