satarupa22/MacromolecularLigandDB huggingface dataset:
MEK1 bound to DS03090629 (PDB entry 7XLP)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 348 residues
Sequence: GLEELELDEQQRKRLEAFLTQKQKVGELKDDDFEKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELMFGCQVEGDAAETPPRPRTPGRPLNKKGMDSRPPMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2186
R free: 0.2462
Average B factor: 63.2445
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.75
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Tris (pH 7.75), 200 mM calcium chloride, 2% DMSO, 18-20% PEG 3350
Matthews coefficient: 2.43
Solvent content (%): 49.39
Ligand: (1~{R},3~{S})-3-[[6-[2-chloranyl-4-(4-methylpyrimidin-2-yl)oxy-phenyl]-3-methyl-1~{H}-indazol-4-yl]oxy]cyclohexan-1-amine (FZC)
Ligand formula: C25 H26 Cl N5 O2
Ligand molecular weight: 463.959
Ligand SMILES: Cc1ccnc(n1)Oc2ccc(c(c2)Cl)c3cc4c(c(n[nH]4)C)c(c3)OC5CCCC(C5)N
Ligand InChI: InChI=1S/C25H26ClN5O2/c1-14-8-9-28-25(29-14)33-19-6-7-20(21(26)13-19)16-10-22-24(15(2)30-31-22)23(11-16)32-18-5-3-4-17(27)12-18/h6-11,13,17-18H,3-5,12,27H2,1-2H3,(H,30,31)/t17-,18+/m1/s1
Release date: 2023-03-01
JMJD2A/ KDM4A COMPLEXED WITH NI(II) AND Macrocyclic PEPTIDE Inhibitor CP2 (13-mer) (PDB entry 5LY1)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 381 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Hetero 5-mer
Stoichiometry: A4, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.178
R free: 0.205
Average B factor: 52
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M propionate-cacodylate-bistris propane pH 9.0 and 25 % w/v polyethylene glycol 1500
Matthews coefficient: 2.47
Solvent content (%): 50.33
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2017-04-12
Crystal Structure of KDM4A with compound YP-03-038 (PDB entry 6G5W)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 359 residues
Sequence: MASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.1763
R free: 0.2177
Average B factor: 44.6793
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 100mM Citrate, 10mM NiCl2, 20% PEG 3350
Matthews coefficient: 2.49
Solvent content (%): 50.63
Ligand: CITRIC ACID (CIT)
Ligand formula: C6 H8 O7
Ligand molecular weight: 192.124
Ligand SMILES: C(C(=O)O)C(CC(=O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)
Release date: 2019-04-10
inhibitors of JumonjiC domain-containing histone demethylases (PDB entry 5ANQ)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.27
Sequence length: 359 residues
Sequence: MASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.18939
R free: 0.23242
Average B factor: 46.636
Crystal growth procedure: 0.233 M LITHIUM SULFATE, 24% PEG 3350, 0.1 M HEPES PH 7.5
Matthews coefficient: 2.59
Solvent content (%): 52
Ligand: 2-{2-[(pyridin-3-ylmethyl)amino]pyrimidin-4-yl}pyridine-4-carboxylic acid (5YQ)
Ligand formula: C16 H13 N5 O2
Ligand molecular weight: 307.307
Ligand SMILES: c1cc(cnc1)CNc2nccc(n2)c3cc(ccn3)C(=O)O
Ligand InChI: InChI=1S/C16H13N5O2/c22-15(23)12-3-6-18-14(8-12)13-4-7-19-16(21-13)20-10-11-2-1-5-17-9-11/h1-9H,10H2,(H,22,23)(H,19,20,21)
Release date: 2016-03-23
Crystal structure of DUSP22 mutant_C88S/S93N (PDB entry 6LOU)
Macromolecule: Dual specificity protein phosphatase 22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 157 residues
Sequence: GPMGNGMNKILPGLYIGNFKDARDAEQLSKNKVTHILSVHDSARPMLEGVKYLCIPAADSPSQNLTRHFKESIKFIHECRLRGESCLVHSLAGVNRSVTLVIAYIMTVTDFGWEDALHTVRAGRSCANPNVGFQRQLQEFEKHEVHQYRQWLKEEYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5301
R work: 0.1717
R free: 0.1957
Average B factor: 19.7138
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.05 M arginine, 0.05 M glutamic acid, 0.4 M NaH2PO4, 1.6 M K2HPO4, 0.2 M NaCl
Matthews coefficient: 2.59
Solvent content (%): 52.55
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: 2020-10-28
Crystal structure of N-truncated human B12 chaperone CblD(C262S)-thiolato-cob(III)alamin complex (108-296) (PDB entry 6X8Z)
Macromolecule: Methylmalonic aciduria and homocystinuria type D protein, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 192 residues
Sequence: GHMSSERHEFVMAQYVNEFQGNDAPVEQEINSAETYFESARVECAIQTCPELLRKDFESLFPEVANGKLMILTVTQKTKNDMTVWSEEVEIEREVLLEKFINGAKEICYALRAEGYWADFIDPSSGLAFFGPYTNNTLFETDERYRHLGFSVDDLGCSKVIRHSLWGTHVVVGSIFTNATPDSHIMKKLSGN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2493
R free: 0.2787
Average B factor: 64.5675
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG8000, 100 mM Tris-HCl, pH 8.5, 200 mM magnesium chloride
Matthews coefficient: 2.6
Solvent content (%): 52.71
Ligand: COBALAMIN (B12)
Ligand formula: C62 H89 Co N13 O14 P
Ligand molecular weight: 1330.356
Ligand SMILES: Cc1cc2c(cc1C)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5C6(C(C(C7=[N]6[Co+2]89[N]5=C4C(=C1[NH]8C(=CC2=[N]9C(=C7C)C(C2CCC(=O)N)(C)CC(=O)N)C(C1CCC(=O)N)(C)C)C)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O
Ligand InChI: InChI=1S/C62H90N13O14P.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;/h20-21,23,28,31,34-37,41,52-53,56-57,72,76,84H,12-19,22,24-27H2,1-11H3,(H2,63,77)(H2,64,78)(H2,65,79)(H2,66,80)(H2,67,81)(H2,68,82)(H,69,83)(H,85,86);/q;+2/b42-23-,50-32-,55-33-;/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;/m1./s1
Release date: 2020-09-16
Crystal structure of the ACVR1 (ALK2) kinase in complex with LDN-212854 (PDB entry 5OXG)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.20611
R free: 0.23243
Average B factor: 45.974
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 18% PEG8000 -- 0.2M calcium acetate -- 0.1M cacodylate pH 6.5
Matthews coefficient: 2.81
Solvent content (%): 56.29
Ligand: 5-[6-(4-piperazin-1-ylphenyl)pyrazolo[1,5-a]pyrimidin-3-yl]quinoline (B4B)
Ligand formula: C25 H22 N6
Ligand molecular weight: 406.482
Ligand SMILES: c1cc(c2cccnc2c1)c3cnn4c3ncc(c4)c5ccc(cc5)N6CCNCC6
Ligand InChI: InChI=1S/C25H22N6/c1-3-21(22-4-2-10-27-24(22)5-1)23-16-29-31-17-19(15-28-25(23)31)18-6-8-20(9-7-18)30-13-11-26-12-14-30/h1-10,15-17,26H,11-14H2
Release date: 2017-09-20
Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors (PDB entry 6P7Z)
Macromolecule: Histone-lysine N-methyltransferase SMYD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 432 residues
Sequence: GSFTMEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.19
R work: 0.1809
R free: 0.1981
Average B factor: 15.2884
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: Sitting drop, room temp, reservoir is 20%PEG 3350, 0.2M MgOAc
protein at 5mg/ml ratio to reservoir is 1:1, seed 
Soaking: 0.1ul of 200mM compound in DMSO added to drop for 72 hours before harvest
Matthews coefficient: 2.19
Solvent content (%): 43.87
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: 2020-01-15
Nicked complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate (PDB entry 4YD2)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 354 residues
Sequence: GSAAASPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.471
R work: 0.2124
R free: 0.2423
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 294
Crystal growth procedure: 0.1M Tris, 20% PEG8K, 0.2M MgCl2
Matthews coefficient: 2.58
Solvent content (%): 52.37
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: 2015-08-05
The FK1 domain of FKBP51 in complex with (3S,11S)-12-((3,5-dichlorophenyl)sulfonyl)-5-oxo-11-vinyldecahydro-1H-6,10-epiminopyrrolo[1,2-a]azonine-3-carboxamide (PDB entry 9EY4)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.16
R work: 0.1424
R free: 0.1686
Average B factor: 14.223
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 34% PEG3350, 0.2M ammonium acetate, 0.1M HEPES-NaOH pH 7.5
Matthews coefficient: 2.31
Solvent content (%): 46.67
Ligand: (1~{S},4~{S},7~{S},8~{S},9~{R})-13-[3,5-bis(chloranyl)phenyl]sulfonyl-8-ethenyl-2-oxidanylidene-3,13-diazatricyclo[7.3.1.0^{3,7}]tridecane-4-carboxamide (A1H78)
Ligand formula: C20 H23 Cl2 N3 O4 S
Ligand molecular weight: 472.385
Ligand SMILES: C=CC1C2CCCC(N2S(=O)(=O)c3cc(cc(c3)Cl)Cl)C(=O)N4C1CCC4C(=O)N
Ligand InChI: InChI=1S/C20H23Cl2N3O4S/c1-2-14-15-6-7-17(19(23)26)24(15)20(27)18-5-3-4-16(14)25(18)30(28,29)13-9-11(21)8-12(22)10-13/h2,8-10,14-18H,1,3-7H2,(H2,23,26)/t14-,15-,16+,17-,18-/m0/s1
Release date: 2024-06-12
Crystal structure of MYST acetyltransferase domain in complex with Acetyl-CoA cofactor (PDB entry 6BA4)
Macromolecule: Histone acetyltransferase KAT8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 295 residues
Sequence: MGSSHHHHHHSSGLVPRGSTKVKYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPPGKEIYRKSNISVHEVDGKDHKIYCQNLCLLAKLFLDHKTLYFDVEPFVFYILTEVDRQGAHIVGYFSKEKESPDGNNVSCIMILPPYQRRGYGRFLIAFSYELSKLESTVGSPEKPLSDLGKLSYRSYWSSVLLENLRDFRGTLSIKDLSQMTSITQNDIISTLQSLNMVKYWKGQHVICVTPKLVEEHLKSAQYKKPPITVDSVCLKWAPPK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.949
R work: 0.1841
R free: 0.2128
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 292
Crystal growth procedure: 2 M NaCl, 0.1 M Tris pH 7.0, 0.22 M MgCl2
Matthews coefficient: 2.34
Solvent content (%): 47.45
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-08-01
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOMB000206a (PDB entry 5QFL)
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): 1.824
R work: 0.1852
R free: 0.2136
Average B factor: 42.0384
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: 3.35
Solvent content (%): 63.26
Ligand: 5-{[4-(trifluoromethyl)phenyl]amino}-1,3,4-thiadiazole-2(3H)-thione (JOM)
Ligand formula: C9 H6 F3 N3 S2
Ligand molecular weight: 277.289
Ligand SMILES: c1cc(ccc1C(F)(F)F)NC2=NNC(=S)S2
Ligand InChI: InChI=1S/C9H6F3N3S2/c10-9(11,12)5-1-3-6(4-2-5)13-7-14-15-8(16)17-7/h1-4H,(H,13,14)(H,15,16)
Release date: 2018-10-10
Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:reaction with 10 mM Mn2+ for 90s (PDB entry 8E8E)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2091
R free: 0.2439
Average B factor: 45.5954
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.07
Solvent content (%): 40.7
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2023-02-01
Crystal structure of CLK1 in complexed with furo[3,2-b]pyridine compound VN345 (derivative of compound 12h) (PDB entry 6I5K)
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): 2.3
R work: 0.19517
R free: 0.22405
Average B factor: 49.003
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 24-28% 1,2-propanediol, 5% glycerol, 0.1M sodium/potassium phosphate
Matthews coefficient: 2.58
Solvent content (%): 52.4
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2019-01-09
Crystal Structure of human phosphodiesterase 10 in complex with 6-methyl-N-(1-propan-2-ylpyrazol-3-yl)-3-(pyrimidin-5-ylamino)pyridine-2-carboxamide (PDB entry 5SKC)
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): 2.6
R work: 0.2161
R free: 0.2423
Average B factor: 73.43
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: 2.69
Solvent content (%): 54.33
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
Structure of Human Aldose Reductase Mutant L300/301A with a Citrate Molecule Bound in the Anion Binding Pocket (PDB entry 6Y03)
Macromolecule: Aldo-keto reductase family 1 member B1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.300
Sequence length: 316 residues
Sequence: MASRILLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCAAASCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1606
R free: 0.1953
Average B factor: 19.87
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Di-Ammoniumhydrogen citrate pH 5: 15 mg/mL hAR, 5,2 mg/mL DTT, 0.7 mg/mL NADP+, 5% (w/v) PEG 6000
Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5, 20% (w/v) PEG 6000
Matthews coefficient: 2.12
Solvent content (%): 42.01
Ligand: CITRIC ACID (CIT)
Ligand formula: C6 H8 O7
Ligand molecular weight: 192.124
Ligand SMILES: C(C(=O)O)C(CC(=O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)
Release date: 2021-02-17
Human GAR transformylase in complex with GAR substrate and AGF131 inhibitor (PDB entry 7JG4)
Macromolecule: Trifunctional purine biosynthetic protein adenosine-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.4.13
Sequence length: 210 residues
Sequence: MARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.455
R work: 0.1875
R free: 0.2545
Average B factor: 55.2894
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris (pH 7.5), 0.333 mM NaCl, 18-22% polyethylene glycol (PEG) 4000, and 2% PEG 400
Matthews coefficient: 3.5
Solvent content (%): 64.87
Ligand: GLYCINAMIDE RIBONUCLEOTIDE (GAR)
Ligand formula: C7 H13 N2 O8 P
Ligand molecular weight: 284.16
Ligand SMILES: C(C1C(C(C(O1)NC(=O)CN)O)O)OP(=O)([O-])[O-]
Ligand InChI: InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/p-2/t3-,5-,6-,7-/m1/s1
Release date: 2021-03-31
Synaptic complex of human DNA polymerase Lambda DL variant engaged on a noncomplementary DNA double-strand break (PDB entry 8U0P)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 340 residues
Sequence: GSAAAVLDKWVCAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQGKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1724
R free: 0.1926
Average B factor: 32.17
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 294
Crystal growth procedure: 85 mM Na cacodylate pH 6.5, 0.17 M ammonium sulfate, 25.5 % (w/v) PEG 8000, 15% (v/v) glycerol
Matthews coefficient: 2.69
Solvent content (%): 54.28
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: 2024-03-13