satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of human PARP-1 CAT domain bound to inhibitor UKTT15 (PDB entry 6VKO)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 372 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMTKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2843
R free: 0.3122
Average B factor: 90.658
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 2M Ammonium Sulfate, Bis-Tris pH6.5
Matthews coefficient: 2.61
Solvent content (%): 52.82
Ligand: methyl 2-{4-[4-(7-carbamoyl-1H-benzimidazol-2-yl)benzene-1-carbonyl]piperazin-1-yl}pyrimidine-5-carboxylate (L1S)
Ligand formula: C25 H23 N7 O4
Ligand molecular weight: 485.495
Ligand SMILES: COC(=O)c1cnc(nc1)N2CCN(CC2)C(=O)c3ccc(cc3)c4[nH]c5c(cccc5n4)C(=O)N
Ligand InChI: InChI=1S/C25H23N7O4/c1-36-24(35)17-13-27-25(28-14-17)32-11-9-31(10-12-32)23(34)16-7-5-15(6-8-16)22-29-19-4-2-3-18(21(26)33)20(19)30-22/h2-8,13-14H,9-12H2,1H3,(H2,26,33)(H,29,30)
Release date: 2020-06-17
Human SLK with SB-440719 (PDB entry 4USF)
Macromolecule: STE20-LIKE SERINE/THREONINE-PROTEIN KINASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 304 residues
Sequence: SMKQYEHVTRDLNPEDFWEIIGELGDGAFGKVYKAQNKETSVLAAAKVIDTKSEEELEDYMVEIDILASCDHPNIVKLLDAFYYENNLWILIEFCAGGAVDAVMLELERPLTESQIQVVCKQTLDALNYLHDNKIIHRDLKAGNILFTLDGDIKLADFGVSAKNTRTIQRRDSFIGTPYWMAPEVVMCETSKDRPYDYKADVWSLGITLIEMAEIEPPHHELNPMRVLLKIAKSEPPTLAQPSRWSSNFKDFLKKCLEKNVDARWTTSQLLQHPFVTVDSNKPIRELIAEAKAEVTEEVEDGKE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.19685
R free: 0.22815
Average B factor: 30.735
Crystallization pH: 6
Crystal growth procedure: 20% PEG6000, 10% ETHYLENE GLYCOL, 0.1 M MES PH 6.0, 0.1 M MGCL2
Matthews coefficient: 2.6
Solvent content (%): 52
Ligand: 4-[4-(6-methoxynaphthalen-2-yl)-1H-imidazol-5-yl]pyridine (6UI)
Ligand formula: C19 H15 N3 O
Ligand molecular weight: 301.342
Ligand SMILES: COc1ccc2cc(ccc2c1)c3c([nH]cn3)c4ccncc4
Ligand InChI: InChI=1S/C19H15N3O/c1-23-17-5-4-14-10-16(3-2-15(14)11-17)19-18(21-12-22-19)13-6-8-20-9-7-13/h2-12H,1H3,(H,21,22)
Release date: 2015-07-22
The double PHD finger (DPF) of MORF in complex with histone H3K14cr (PDB entry 6OIE)
Macromolecule: Histone acetyltransferase KAT6B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 116 residues
Sequence: GSHMDPIPICSFCLGTKESNREKKPEELLSCADCGSSGHPSCLKFCPELTTNVKALRWQCIECKTCSACRVQGRNADNMLFCDSCDRGFHMECCDPPLSRMPKGMWICQVCRPKKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.075
R work: 0.1659
R free: 0.2191
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 1.1-1.3 M sodium citrate tribasic and 0.1 M sodium hepes
Matthews coefficient: 2.6
Solvent content (%): 52.72
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: 2019-11-20
Crystal structure of hMTH1 D120N in complex with TH scaffold 1 in the absence of acetate (PDB entry 6GLV)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 182 residues
Sequence: MKHHHHHHPMSDYDIPTTENLYFQGAMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDNSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.601
R work: 0.1771
R free: 0.2163
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: crystallized in: 23-27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5

soaked in: 0.27 M ammonium sulfate, 17% glycerol, 27% PEG4000, 50 mM compound
Solvent content (%): 27.32
Ligand: 4-phenylpyrimidin-2-amine (F3E)
Ligand formula: C10 H9 N3
Ligand molecular weight: 171.199
Ligand SMILES: c1ccc(cc1)c2ccnc(n2)N
Ligand InChI: InChI=1S/C10H9N3/c11-10-12-7-6-9(13-10)8-4-2-1-3-5-8/h1-7H,(H2,11,12,13)
Release date: 2019-02-20
Structure of CC Chemokine Receptor 2 with Orthosteric and Allosteric Antagonists (PDB entry 5T1A)
Macromolecule: Chimera protein of CC chemokine receptor type 2 isoform B and T4-lysozyme,Lysozyme
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 508 residues
Sequence: DYKDDDDKPGTLSTSRSRFIRNTNESGEEVTTFFDYDYGAPCHKFDVKQIGAQLLPPLYSLVFIFGFVGNMLVVLILINCKKLKCLTDIYLLNLAISDLLFLITLPLWAHSAANEWVFGNAMCKLFTGLYHIGYFGGIFFIILLTIDRYLAIVHAVFALKARTVTFGVVTSVITWLVAVFASVPGIIFTKCQKEDSVYVCGPYFPRGWNNFHTIMRNILGLVLPLLIMVICYSGISRASKSRINIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYPPPSREKKAVRVIFTIMIVYFLFWTPYNIVILLNTFQEFFGLSNCESTSQLDQATQVTETLGMTHCCINPIIYAFVGEKFRRYLSVFFRKHITKRFGRPLEVLFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.806
R work: 0.2335
R free: 0.2741
Average B factor: 41.2114
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 6.1
Crystallization temperature (K): 295
Crystal growth procedure: Lipidic cubic phase made of monoolein and cholesterol, 100 mM 2-(N-morpholino)ethanesulfonic acid, pH 6.5, 30-32% (v/v) PEG 400, 75-85 mM lithium sulfate
Matthews coefficient: 2.81
Solvent content (%): 61.86
Ligand: (3S)-1-{(1S,2R,4R)-4-[methyl(propan-2-yl)amino]-2-propylcyclohexyl}-3-{[6-(trifluoromethyl)quinazolin-4-yl]amino}pyrrolidin-2-one (73R)
Ligand formula: C26 H36 F3 N5 O
Ligand molecular weight: 491.592
Ligand SMILES: CCCC1CC(CCC1N2CCC(C2=O)Nc3c4cc(ccc4ncn3)C(F)(F)F)N(C)C(C)C
Ligand InChI: InChI=1S/C26H36F3N5O/c1-5-6-17-13-19(33(4)16(2)3)8-10-23(17)34-12-11-22(25(34)35)32-24-20-14-18(26(27,28)29)7-9-21(20)30-15-31-24/h7,9,14-17,19,22-23H,5-6,8,10-13H2,1-4H3,(H,30,31,32)/t17-,19-,22+,23+/m1/s1
Release date: 2016-12-14
SMYD2 in complex with AZ370 (PDB entry 5KJK)
Macromolecule: N-lysine methyltransferase SMYD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 429 residues
Sequence: GLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLEFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIESH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.178
R free: 0.203
Average B factor: 41.28
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 0.1 M Tris-HCl, 5% ethanol
Matthews coefficient: 3.23
Solvent content (%): 61.91
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2016-12-07
JAK2 kinase (JH1 domain) mutant P1057A in complex with TG101209 (PDB entry 5HEZ)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 302 residues
Sequence: GSSGAFEDRDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSAPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.66
R work: 0.2169
R free: 0.2384
Average B factor: 67.77
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 1.9 M sodium malonate, 10 mM ZnCl2
Matthews coefficient: 3.68
Solvent content (%): 66.6
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: 2016-11-09
Crystal structure of human CPSF73 catalytic segment in complex with compound 1 (PDB entry 8T1Q)
Macromolecule: Cleavage and polyadenylation specificity factor subunit 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27
Sequence length: 479 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMSAIPAEESDQLLIRPLGAGQEVGRSCIILEFKGRKIMLDCGIHPGLEGMDALPYIDLIDPAEIDLLLISHFHLDHCGALPWFLQKTSFKGRTFMTHATKAIYRWLLSDYVKVSNISADDMLYTETDLEESMDKIETINFHEVKEVAGIKFWCYHAGHVLGAAMFMIEIAGVKLLYTGDFSRQEDRHLMAAEIPNIKPDILIIESTYGTHIHEKREEREARFCNTVHDIVNRGGRGLIPVFALGRAQELLLILDEYWQNHPELHDIPIYYASSLAKKCMAVYQTYVNAMNDKIRKQININNPFVFKHISNLKSMDHFDDIGPSVVMASPGMMQSGLSRELFESWCTDKRNGVIIAGYCVEGTLAKHIMSEPEEITTMSGQKLPLKMSVDYISFSAHTDYQQTSEFIRALKPPHVILVHGEQNEMARLKAALIREYEDNDEVHIEVHNPRNTEAVTLNFR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1833
R free: 0.2149
Average B factor: 42.08
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 18-30% (w/v) PEG3350, 200-250 mM ammonium sulfate and 0.1 M Bis-Tris pH 6.3-6.7
Matthews coefficient: 2.29
Solvent content (%): 46.22
Ligand: 3-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-5-yl]-~{N}-[3-(4-ethanoylphenyl)phenyl]propanamide (XYX)
Ligand formula: C24 H23 B N O5
Ligand molecular weight: 416.254
Ligand SMILES: [B-]1(c2c(cccc2CCC(=O)Nc3cccc(c3)c4ccc(cc4)C(=O)C)CO1)(O)O
Ligand InChI: InChI=1S/C24H23BNO5/c1-16(27)17-8-10-18(11-9-17)20-5-3-7-22(14-20)26-23(28)13-12-19-4-2-6-21-15-31-25(29,30)24(19)21/h2-11,14,29-30H,12-13,15H2,1H3,(H,26,28)/q-1
Release date: 2023-11-08
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000232a (PDB entry 5QE9)
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): 1.692
R work: 0.1863
R free: 0.2068
Average B factor: 40.0685
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: 3.33
Solvent content (%): 63.05
Ligand: 4-chloro-N-cyclopentyl-1-methyl-1H-pyrazole-3-carboxamide (JHP)
Ligand formula: C10 H14 Cl N3 O
Ligand molecular weight: 227.691
Ligand SMILES: Cn1cc(c(n1)C(=O)NC2CCCC2)Cl
Ligand InChI: InChI=1S/C10H14ClN3O/c1-14-6-8(11)9(13-14)10(15)12-7-4-2-3-5-7/h6-7H,2-5H2,1H3,(H,12,15)
Release date: 2018-10-10
Crystal structure of the second bromodomain (BD2) of human TAF1 bound to ZS1-322 (PDB entry 7JTC)
Macromolecule: Transcription initiation factor TFIID subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 137 residues
Sequence: SMDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELESLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2015
R free: 0.2317
Average B factor: 47.7817
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.01 M Co(II) chloride, 0.1 M Sodium acetate trihydrate (pH 4.6), 1 M 1,6-Hexanediol
Matthews coefficient: 2.47
Solvent content (%): 50.28
Ligand: 1-{6-[(3R)-3-methylmorpholin-4-yl]-2-(methylsulfanyl)pyrimidin-4-yl}cyclopropane-1-sulfonimidoamide (VK1)
Ligand formula: C13 H21 N5 O2 S2
Ligand molecular weight: 343.468
Ligand SMILES: CC1COCCN1c2cc(nc(n2)SC)C3(CC3)S(=N)(=O)N
Ligand InChI: InChI=1S/C13H21N5O2S2/c1-9-8-20-6-5-18(9)11-7-10(16-12(17-11)21-2)13(3-4-13)22(14,15)19/h7,9H,3-6,8H2,1-2H3,(H3,14,15,19)/t9-/m1/s1
Release date: 2021-08-25
Crystal structure of T110A:S256A mutant human Glutamate oxaloacetate transaminase 1 (GOT1) (PDB entry 6DNB)
Macromolecule: Aspartate aminotransferase, cytoplasmic
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.6.1.1
Sequence length: 411 residues
Sequence: PPSVFAEVPQAQPVLVFKLTADFREDPDPRKVNLGVGAYRTDDCHPWVLPVVKKVEQKIANDNSLNHEYLPILGLAEFRSCASRLALGDDSPALKEKRVGGVQSLGGAGALRIGADFLARWYNGTNNKNTPVYVSSPTWENHNAVFSAAGFKDIRSYRYWDAEKRGLDLQGFLNDLENAPEFSIVVLHACAHNPTGIDPTPEQWKQIASVMKHRFLFPFFDSAYQGFASGNLERDAWAIRYFVSEGFEFFCAQAFSKNFGLYNERVGNLTVVGKEPESILQVLSQMEKIVRITWSNPPAQGARIVASTLSNPELFEEWTGNVKTMADRILTMRSELRARLEALKTPGTWIHITDQIGMFSFTGLNPKQVEYLVNEKHIYLLPSGRINVSGLTTKNLDYVATSIHEAVTKIQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.179
R free: 0.22873
Average B factor: 24.887
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Tris pH 8.5, 20% w/v/ PEG MME 2,000, 0.2 M Trimethylamine N-oxide dehydrate
Matthews coefficient: 2.32
Solvent content (%): 47.04
Ligand: TETRAETHYLENE GLYCOL (PG4)
Ligand formula: C8 H18 O5
Ligand molecular weight: 194.226
Ligand SMILES: C(COCCOCCOCCO)O
Ligand InChI: InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2
Release date: 2018-11-14
Structure of HDAC2 in complex with an inhibitor (compound 9) (PDB entry 7MOT)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 376 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.54
R work: 0.1781
R free: 0.2032
Average B factor: 22.81
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
Matthews coefficient: 2.47
Solvent content (%): 50.28
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: 2021-07-14
Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor Gp5A (PDB entry 6ZJB)
Macromolecule: GTP:AMP phosphotransferase AK3, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.4.10
Sequence length: 227 residues
Sequence: MGASARLLRAVIMGAPGSGKGTVSSRITTHFELKHLSSGDLLRDNMLRGTEIGVLAKAFIDQGKLIPDDVMTRLALHELKNLTQYSWLLDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIKQRLTARWIHPASGRVYNIEFNPPKTVGIDDLTGEPLIQREDDKPETVIKRLKAYEDQTKPVLEYYQKKGVLETFSGTETNKIWPYVYAFLQTKVPQRSQKASVTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.822
R work: 0.1916
R free: 0.2565
Average B factor: 37.9739
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 291
Crystal growth procedure: Purified hAK3 was dialyzed against 30 mM MOPS buffer with 50 mM NaCl pH 7.0 and concentrated to 15-20 mg per ml. The resevoir contained 20% isopropanol, 0.1 M NaCitrate pH 5.6 and 20% PEG 4000. Drop size 1 plus 1 microliter.
Matthews coefficient: 2.08
Solvent content (%): 40.96
Ligand: P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE (G5P)
Ligand formula: C20 H29 N10 O23 P5
Ligand molecular weight: 932.366
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O)N
Ligand InChI: InChI=1S/C20H29N10O23P5/c21-14-8-15(24-3-23-14)29(4-25-8)18-12(33)10(31)6(48-18)1-46-54(36,37)50-56(40,41)52-58(44,45)53-57(42,43)51-55(38,39)47-2-7-11(32)13(34)19(49-7)30-5-26-9-16(30)27-20(22)28-17(9)35/h3-7,10-13,18-19,31-34H,1-2H2,(H,36,37)(H,38,39)(H,40,41)(H,42,43)(H,44,45)(H2,21,23,24)(H3,22,27,28,35)/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1
Release date: 2020-09-16
CDK6 in complex with Cpd24 N-(5-(6-ethyl-2,6-diazaspiro[3.3]heptan-2-yl)pyridin-2-yl)-5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl)pyrimidin-2-amine (PDB entry 6OQO)
Macromolecule: Cyclin-dependent kinase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 291 residues
Sequence: QQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVQTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDRETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLDFLHSHRVVHRDLKPQNILVTSSGQIKLADFGLARIYSFQMALTSVVVTLWYRAPEVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILDVIGLPGEEDWPRDVALPRQAFHSKSAQPIEKFVTDIDELGKDLLLKCLTFNPAKRISAYSALSHPYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.977
R work: 0.2155
R free: 0.2641
Average B factor: 73.8988
Crystallization method: EVAPORATION
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 17 % w/v PEG 3,350, 100 mM HEPES, pH 7.5, 200 mM NaCl, 20 mM L-Glutathione
Matthews coefficient: 2.63
Solvent content (%): 53.22
Ligand: N-[5-(6-ethyl-2,6-diazaspiro[3.3]heptan-2-yl)pyridin-2-yl]-5-fluoro-4-[(4R)-4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl]pyrimidin-2-amine (N1J)
Ligand formula: C25 H31 F N8
Ligand molecular weight: 462.566
Ligand SMILES: CCN1CC2(C1)CN(C2)c3ccc(nc3)Nc4ncc(c(n4)c5cnn6c5C(CCCC6)C)F
Ligand InChI: InChI=1S/C25H31FN8/c1-3-32-13-25(14-32)15-33(16-25)18-7-8-21(27-10-18)30-24-28-12-20(26)22(31-24)19-11-29-34-9-5-4-6-17(2)23(19)34/h7-8,10-12,17H,3-6,9,13-16H2,1-2H3,(H,27,28,30,31)/t17-/m1/s1
Release date: 2020-07-29
Crystal structure of monomeric FICD mutant L258D complexed with MgAMP-PNP (PDB entry 6I7L)
Macromolecule: Adenosine monophosphate-protein transferase FICD
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7
Sequence length: 343 residues
Sequence: SLEARAALNQALEMKRQGKREKAQKLFMHALKMDPDFVDALTEFGIFSEEDKDIIQADYLYTRALTISPYHEKALVNRDRTLPLVEEIDQRYFSIIDSKVKKVMSIPKGNSALRRVMEETYYHHIYHTVAIEGNTLTLSEIRHILETRYAVPGKSDEEQNEVIGMHAAMKYINTTLVSRIGSVTISDVLEIHRRVLGYVDPVEAGRFRTTQVLVGHHIPPHPQDVEKQMQEFVQWLNSEEAMNLHPVEFAALAHYKLVYIHPFIDGNGRTSRLLMNLILMQAGYPPITIRKEQRSDYYHVLEAANEGDVRPFIRFIAKCTETTLDTLLFATTEYSVALPEAQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.32
R work: 0.21453
R free: 0.25095
Average B factor: 56.459
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.5 M Sodium Chloride; 10% Ethanol
Matthews coefficient: 4.95
Solvent content (%): 75.19
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2019-09-25
Human DNA polymerase eta-DNA-dGMPNPP ternary mismatch complex in 2.0 mM Mg2+ for 600s (PDB entry 7U7X)
Macromolecule: DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 12 residues
Sequence: CATTATGACGCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1886
R free: 0.2098
Average B factor: 33.4301
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.09
Solvent content (%): 41.14
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: 2022-05-04
DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 20 min (PDB entry 7M4A)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 329 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.868
R work: 0.1875
R free: 0.2202
Average B factor: 50.2203
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.84
Solvent content (%): 56.74
Ligand: PYROPHOSPHATE (PPV)
Ligand formula: H4 O7 P2
Ligand molecular weight: 177.975
Ligand SMILES: OP(=O)(O)OP(=O)(O)O
Ligand InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)
Release date: 2022-07-06
Crystal structure of hMTH1 in complex with TH scaffold 1 in the presence of acetate (PDB entry 6GLE)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 182 residues
Sequence: MKHHHHHHPMSDYDIPTTENLYFQGAMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.402
R work: 0.1875
R free: 0.2151
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: crystallized in: 23-27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5

soaked in: 27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5, 20% DMSO, 10 mM compound
Matthews coefficient: 1.71
Solvent content (%): 28.15
Ligand: 4-phenylpyrimidin-2-amine (F3E)
Ligand formula: C10 H9 N3
Ligand molecular weight: 171.199
Ligand SMILES: c1ccc(cc1)c2ccnc(n2)N
Ligand InChI: InChI=1S/C10H9N3/c11-10-12-7-6-9(13-10)8-4-2-1-3-5-8/h1-7H,(H2,11,12,13)
Release date: 2019-02-20