satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of MAP4K1 with a SMOL inhibitor (PDB entry 8PAU)
Macromolecule: Mitogen-activated protein kinase kinase kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 288 residues
Sequence: DIFNRDPRDHYDLLQRLGGGTYGEVFKARDKVSGDLVALKMVKMEPDDDVSTLQKEILILKTCRHANIVAYHGSYLWLQKLWICMEFCGAGSLQDIYQVTGSLSELQISYVCREVLQGLAYLHSQKKIHRDIKGANILINDAGEVRLADFGISAQIGATLARRLSFIGTPYWMAPEVAAVALKGGYNELCDIWSLGITAIELAELQPPLFDVHPLRVLFLMTKSGYQPPRLKEKGKWSAAFHNFIKVTLTKSPKKRPSATKMLSHQLVSQPGLNRGLILDLLDKLKNP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.21667
R free: 0.2723
Average B factor: 77.824
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: NOT DISCLOSED
Matthews coefficient: 2.82
Solvent content (%): 56.36
Ligand: [(5~{R})-2-[[3,5-bis(fluoranyl)-4-[[3-(trifluoromethyl)-1~{H}-pyrrolo[2,3-b]pyridin-4-yl]oxy]phenyl]amino]-5-fluoranyl-4,6-dihydro-1,3-oxazin-5-yl]methanol (XOR)
Ligand formula: C19 H14 F6 N4 O3
Ligand molecular weight: 460.33
Ligand SMILES: c1cnc2c(c1Oc3c(cc(cc3F)NC4=NCC(CO4)(CO)F)F)c(c[nH]2)C(F)(F)F
Ligand InChI: InChI=1S/C19H14F6N4O3/c20-11-3-9(29-17-28-6-18(22,7-30)8-31-17)4-12(21)15(11)32-13-1-2-26-16-14(13)10(5-27-16)19(23,24)25/h1-5,30H,6-8H2,(H,26,27)(H,28,29)/t18-/m1/s1
Release date: 2024-06-26
The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with human ISG15 (PDB entry 7RBS)
Macromolecule: Papain-like protease
Type: Protein, polypeptide(L)
Source organism: Severe acute respiratory syndrome coronavirus 2
EC number: 3.4.19.12
Sequence length: 318 residues
Sequence: SNAEVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.98
R work: 0.1951
R free: 0.2358
Average B factor: 76.102
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.02 M MgCl2, 0.1 M HEPES buffer, 22% poly(acrylicacid sodium salt) 5100
Matthews coefficient: 3.71
Solvent content (%): 66.85
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: 2021-09-29
Monobody Mb(Lck_3) bound to Lck-SH2 domain (PDB entry 5MTM)
Macromolecule: Tyrosine-protein kinase Lck
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 116 residues
Sequence: GSKANSLEPEPWFFKNLSRKDAERQLLAPGNTHGSFLIRESESTAGSFSLSVRDFDQNQGEVVKHYKIRNLDNGGFYISPRITFPGLHELVRHYTNASDGLCTRLSRPCQTQKPQK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.405
R work: 0.2054
R free: 0.2568
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MES pH6.5, 15 % PEG 20000
Matthews coefficient: 3.81
Solvent content (%): 67.72
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: 2017-04-05
Crystal Structure of the Human vaccinia-related kinase bound to a propynyl-pteridinone inhibitor (PDB entry 6CFM)
Macromolecule: Serine/threonine-protein kinase VRK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.20114
R free: 0.2446
Average B factor: 40.305
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Matthews coefficient: 3
Solvent content (%): 59.01
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
Crystal Structure of human Pin1 complexed with a covalent inhibitor (PDB entry 7EKV)
Macromolecule: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 183 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMADEEKLPPGWEKAMSRSSGRVYYFNHITNASQWERPSGNSSSGGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1974
R free: 0.2349
Average B factor: 20.1142
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277.15
Crystal growth procedure: 2M Ammonium Sulfate, 1% PEG400, 100mM HEPES, pH 7.5
Matthews coefficient: 2.67
Solvent content (%): 58.15
Ligand: 8-(2-chloroacetyl)-4-((5-phenylfuran-2-yl)methyl)-1-thia-4,8-diazaspiro[4.5]decan-3-one (J50)
Ligand formula: C20 H21 Cl N2 O3 S
Ligand molecular weight: 404.91
Ligand SMILES: c1ccc(cc1)c2ccc(o2)CN3C(=O)CSC34CCN(CC4)C(=O)CCl
Ligand InChI: InChI=1S/C20H21ClN2O3S/c21-12-18(24)22-10-8-20(9-11-22)23(19(25)14-27-20)13-16-6-7-17(26-16)15-4-2-1-3-5-15/h1-7H,8-14H2
Release date: 2022-02-16
Crystal structure of fragment 3-(3-Methoxy-2-quinoxalinyl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain (PDB entry 6CEC)
Macromolecule: Histone deacetylase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 107 residues
Sequence: GSPLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNKFGEDMPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1619
R free: 0.186
Average B factor: 15.839
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 291
Crystal growth procedure: 2 M Na-formate, 0.2 M Na-acetate pH4.6, 5 % ethylene glycol
Matthews coefficient: 2.09
Solvent content (%): 41.07
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: 2018-02-28
Discovery of IRAK4 Inhibitors BAY1834845 and BAY1830839 (PDB entry 8BR7)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 298 residues
Sequence: GSFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIAAAIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.119
R work: 0.2387
R free: 0.2879
Average B factor: 60.235
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M sodium acetate buffer at pH 4.9, 1.5-1.7M ammonium citrate and 0.02M hexaaminecobalt(III)chloride
Matthews coefficient: 2.7
Solvent content (%): 54.5
Ligand: 3-nitro-~{N}-[2-[2-oxidanylidene-2-[4-(phenylcarbonyl)piperazin-1-yl]ethyl]indazol-5-yl]benzamide (R6R)
Ligand formula: C27 H24 N6 O5
Ligand molecular weight: 512.517
Ligand SMILES: c1ccc(cc1)C(=O)N2CCN(CC2)C(=O)Cn3cc4cc(ccc4n3)NC(=O)c5cccc(c5)N(=O)=O
Ligand InChI: InChI=1S/C27H24N6O5/c34-25(30-11-13-31(14-12-30)27(36)19-5-2-1-3-6-19)18-32-17-21-15-22(9-10-24(21)29-32)28-26(35)20-7-4-8-23(16-20)33(37)38/h1-10,15-17H,11-14,18H2,(H,28,35)
Release date: 2024-01-31
EGFR(T790M/V948R) in complex with LN5461 (PDB entry 8TO3)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 328 residues
Sequence: SGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.49
R work: 0.2292
R free: 0.2687
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: Bis-Tris (100mM), 25% PEG-3350 and TCEP (5mM)
Matthews coefficient: 2.07
Solvent content (%): 40.61
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: 2024-08-28
HUMAN CARBONIC ANHYDRASE VII IN COMPLEX WITH A SULFONAMIDE INHIBITOR (PDB entry 6SDT)
Macromolecule: Carbonic anhydrase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 274 residues
Sequence: MGMTGHHGWGYGQDDGPSHWHKLYPIAQGDRQSPINIISSQAVYSPSLQPLELSYEACMSLSITNNGHSVQVDFNDSDDRTVVTGGPLEGPYRLKQFHFHWGKKHDVGSEHTVDGKSFPSELHLVHWNAKKYSTFGEAASAPDGLAVVGVFLETGDEHPSMNRLTDALYMVRFKGTKAQFSCFNPKSLLPASRHYWTYPGSLTTPPLSESVTWIVLREPISISERQMGKFRSLLFTSEDDERIHMVNNFRPPQPLKGRVVKASFRALEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.1877
R free: 0.2257
Average B factor: 20.985
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% (W/V) POLYETHYLENE GLYCOL 3350, 0.2 M AMMONIUM ACETATE, 0.1 M TRIS-HCL,
Matthews coefficient: 2.11
Solvent content (%): 41.83
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-06-10
Crystal structure of SIRT3 in complex with H3K23la peptide (PDB entry 8HLY)
Macromolecule: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 281 residues
Sequence: DKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1559
R free: 0.2026
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M BIS-TRIS pH at 6.5, 28% (w/v) Polyethylene glycol monomethyl ether 2000
Matthews coefficient: 2
Solvent content (%): 38.44
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: 2023-09-27
DCN1 bound to DI-1548 (PDB entry 6XOL)
Macromolecule: Lysozyme, DCN1-like protein 1 chimera
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 386 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSNAMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWAEAAVNLAKSRWYNQTPNRTKRVITTFATGTWDAYKNLRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.39
R work: 0.212
R free: 0.264
Average B factor: 42.34
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 28-33 % PEG3350, 200 mM ammonium formate
Matthews coefficient: 2.21
Solvent content (%): 44.3
Ligand: N-{(1S)-1-cyclohexyl-2-[(2-methylpropanoyl)amino]ethyl}-N~2~-propanoyl-3-[6-(propan-2-yl)-1,3-benzothiazol-2-yl]-L-alaninamide (H8S)
Ligand formula: C28 H42 N4 O3 S
Ligand molecular weight: 514.723
Ligand SMILES: CCC(=O)NC(Cc1nc2ccc(cc2s1)C(C)C)C(=O)NC(CNC(=O)C(C)C)C3CCCCC3
Ligand InChI: InChI=1S/C28H42N4O3S/c1-6-25(33)30-22(15-26-31-21-13-12-20(17(2)3)14-24(21)36-26)28(35)32-23(16-29-27(34)18(4)5)19-10-8-7-9-11-19/h12-14,17-19,22-23H,6-11,15-16H2,1-5H3,(H,29,34)(H,30,33)(H,32,35)/t22-,23+/m0/s1
Release date: 2021-06-02
Crystal Structure of CK2alpha with Compound 6 bound (PDB entry 5CSV)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.375
R work: 0.1795
R free: 0.195
Average B factor: 25.17
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.01
Solvent content (%): 38.71
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2016-07-27
Crystal structure of DAPK1 in complex with morin. (PDB entry 5AUY)
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): 2
R work: 0.2066
R free: 0.2493
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2 M ammonium sulfate, 0.1 M MES
Matthews coefficient: 1.9
Solvent content (%): 35.38
Ligand: 2-[2,4-bis(oxidanyl)phenyl]-3,5,7-tris(oxidanyl)chromen-4-one (MRI)
Ligand formula: C15 H10 O7
Ligand molecular weight: 302.236
Ligand SMILES: c1cc(c(cc1O)O)C2=C(C(=O)c3c(cc(cc3O2)O)O)O
Ligand InChI: InChI=1S/C15H10O7/c16-6-1-2-8(9(18)3-6)15-14(21)13(20)12-10(19)4-7(17)5-11(12)22-15/h1-5,16-19,21H
Release date: 2015-10-07
Crystal structure of the N-terminal domain of the human mitochondrial calcium uniporter fused with T4 lysozyme (PDB entry 4XSJ)
Macromolecule: Lysozyme,Calcium uniporter protein, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 262 residues
Sequence: MNIFEMLRIDEGLRLKIYKNTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYGSVTVVYQNGLPVISVRLPSRRERCQFTLKPISDSVGVFLRQLQEEDRGIDRVAIYSPDGVRVAASTGIDLLLLDDFKLVINDLTYHVRPPKRLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.127
R free: 0.19
Average B factor: 29.253
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 5% glycerol, 0.3 M ammonium sulphate and 0.1 M Bis-Tris-HCl (pH 5.5)
Matthews coefficient: 2.91
Solvent content (%): 57.72
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: 2015-09-16
Notum Inhibitor ARUK3004556 (PDB entry 8BTI)
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): 1.31
R work: 0.1844
R free: 0.2183
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: 1.93
Solvent content (%): 36.23
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: 2022-12-14
DNA Polymerase Beta I260Q Binary Complex (PDB entry 6BTE)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLQPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1852
R free: 0.229
Average B factor: 18.9345
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 18-20% PEG 3350, 175-250 mM sodium acetate, 50 mM HEPES pH 7.5, 2 mM TCEP, 1% tert-butanol
Matthews coefficient: 2.26
Solvent content (%): 45.49
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-09-26
E3 RING ligase binding domain (PDB entry 7OVX)
Macromolecule: E3 ubiquitin-protein ligase TRIM7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 174 residues
Sequence: HHHMVELTLDPDTANPRLILSLDLKSVRLGQRAQDLPNHPRRFDTNTRVLASCGFSSGRHHWEVEVGSKDGWAFGVARESVRRKGLTPFTPEEGVWAMQLNNGQYWAVTSPERTQLNCGHLSRVRVALDLEVGAVSFYAVEDMRHLYTFRVNFQERVFPLFSVCSTGTYLRIWP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1835
R free: 0.2259
Average B factor: 22.93
Crystallization method: BATCH MODE
Crystallization temperature (K): 296
Crystal growth procedure: 20% PEG 4K, 0.1M NaCl, 50 mM HEPES pH7
Matthews coefficient: 1.94
Solvent content (%): 36.44
Release date: 2022-06-22
Ternary complex crystal structure of DNA polymerase Beta with G:T mismatch at the primer terminus (PDB entry 5J2H)
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): 2.3
R work: 0.2051
R free: 0.2664
Average B factor: 30.1557
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
Matthews coefficient: 2.3
Solvent content (%): 46.42
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: 2016-10-26
Crystal structure of human GPX4-U46C (PDB entry 7L8K)
Macromolecule: Phospholipid hydroperoxide glutathione peroxidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.1.12
Sequence length: 192 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMLEAASRDDWRCARSMHEFSAKDIDGHMVNLDKYRGFVCIVTNVASQCGKTEVNYTQLVDLHARYAECGLRILAFPCNQFGKQEPGSNEEIKEFAAGYNVKFDMFSKICVNGDDAHPLWKWMKIQPKGKGILGNAIKWNFTKFLIDKNGCVVKRYGPMEEPLVIEKDLPHYF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.38
R work: 0.1469
R free: 0.1651
Average B factor: 20.3969
Crystallization method: MICROBATCH
Crystallization pH: 8.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.056 M sodium phosphate monobasic monohydrate and 1.344 M potassium phosphate
Matthews coefficient: 1.66
Solvent content (%): 25.69
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: 2021-12-29
FACTOR XIA IN COMPLEX WITH THE INHIBITOR METHYL ((15S)-15-(((2E)-3-(5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL)-2-PROPENOYL)AMINO)-9-OXO-8,17,19-TRIAZATRICYCLO[14.2.1.0~2,7~]NONADECA-1(18),2,4,6,16(19)-PENTAEN-5-YL)CARBAMATE (PDB entry 5TKU)
Macromolecule: Factor XIa (Light Chain)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.1664
R free: 0.1846
Average B factor: 25.53
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 100 MM SODIUM ACETATE, PH 4.6, 25%(w/v) MEPEG2000, 200 MM AMMONIUM SULFATE, then transferred to 100 MM TRIS-HCL, pH 7.0, 25%(w/v) MEPEG2000, 200 MM AMMONIUM SULFATE
Matthews coefficient: 3.43
Solvent content (%): 64.11
Ligand: METHYL
((15S)-15-(((2E)-3-(5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL)-2-PROPENOYL)AMINO)-9-OXO-8,17,19-TRIAZATRICYCLO[14.2.1.0~2,7~]N
ONADECA-1(18),2,4,6,16(19)-PENTAEN-5-YL)CARBAMATE (7DK)
Ligand formula: C28 H28 Cl N9 O4
Ligand molecular weight: 590.033
Ligand SMILES: COC(=O)Nc1ccc-2c(c1)NC(=O)CCCCCC(c3[nH]cc2n3)NC(=O)C=Cc4cc(ccc4n5cnnn5)Cl
Ligand InChI: InChI=1S/C28H28ClN9O4/c1-42-28(41)32-19-9-10-20-22(14-19)34-25(39)6-4-2-3-5-21(27-30-15-23(20)35-27)33-26(40)12-7-17-13-18(29)8-11-24(17)38-16-31-36-37-38/h7-16,21H,2-6H2,1H3,(H,30,35)(H,32,41)(H,33,40)(H,34,39)/b12-7+/t21-/m0/s1
Release date: 2017-03-01