satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of M1-StaR-T4L in complex with GSK1034702 at 2.5A (PDB entry 6ZG9)
Macromolecule: Muscarinic acetylcholine receptor M1,Endolysin,Muscarinic acetylcholine receptor M1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 455 residues
Sequence: METVEMVAIATVAGLLSLATVTGNILLMLSIKVNRQLQTVNNYFAFSLACADLIIGAFSMNLYTVYIIMGHWALGALACDLALALDYVASNAAVMNLLLISFDRYFSVTRPLSYRAKRTPRRALLMIGLAWLVSFVLWAPAILFWQYLVGERTVLAGQCYIQFLSQPIITFGTAMATFYLPVTVMCTLYWRIYRETENRANIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYTFSLVKEKAALRTLSAILLAFILTWTPYNIMVLVSTFCKDCVPETLWELGYWLCYVNATINPMCYALCNKAFRDTFRLLLLARWDHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.203
R free: 0.242
Average B factor: 52.08
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 NaHEPES pH 7.4-7.8, 0.1M di-ammonium hydrogenohosphate, 30-38% PEG300
Matthews coefficient: 3.16
Solvent content (%): 61.08
Ligand: 7-fluoranyl-5-methyl-3-[1-(oxan-4-yl)piperidin-4-yl]-1~{H}-benzimidazol-2-one (QK2)
Ligand formula: C18 H24 F N3 O2
Ligand molecular weight: 333.4
Ligand SMILES: Cc1cc2c(c(c1)F)NC(=O)N2C3CCN(CC3)C4CCOCC4
Ligand InChI: InChI=1S/C18H24FN3O2/c1-12-10-15(19)17-16(11-12)22(18(23)20-17)14-2-6-21(7-3-14)13-4-8-24-9-5-13/h10-11,13-14H,2-9H2,1H3,(H,20,23)
Release date: 2021-10-06
Human DYRK2 bound to Curcumin (PDB entry 6HDR)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 429 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMGKVKATPMTPEQAMKQYMQKLTAFEHHEIFSYPEIYFLGLNAKKRQGMTGGPNNGGYDDDQGSYVQVPHDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTYIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRRLPKPPTGEKTSVKR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.18974
R free: 0.24263
Average B factor: 72.456
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M sodium potassium phosphate,  20% PEG 3350 and  10% ethylene glycol
Matthews coefficient: 2.63
Solvent content (%): 53.15
Ligand: curcumin (CC9)
Ligand formula: C21 H20 O6
Ligand molecular weight: 368.38
Ligand SMILES: COc1cc(ccc1O)C=CC(=O)CC(=O)C=Cc2ccc(c(c2)OC)O
Ligand InChI: InChI=1S/C21H20O6/c1-26-20-11-14(5-9-18(20)24)3-7-16(22)13-17(23)8-4-15-6-10-19(25)21(12-15)27-2/h3-12,24-25H,13H2,1-2H3/b7-3+,8-4+
Release date: 2019-08-28
XChem fragment screen -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF THE HUMAN ATAD2 in complex with N13501a (PDB entry 5R4W)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYRTVIKEPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47
R work: 0.1277
R free: 0.1612
Average B factor: 25.049
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 2.2M ammonium sulfate, 0.1M bis-tris pH 5.5
Matthews coefficient: 4.2
Solvent content (%): 70.7
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: 2020-05-13
Human Brr2 Helicase Region in complex with C-tail deleted Jab1 (PDB entry 6S8Q)
Macromolecule: U5 small nuclear ribonucleoprotein 200 kDa helicase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 1747 residues
Sequence: GAEFMDLDQGGEALAPRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPALKPKPFGSEEQLLPVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRRLDLVHTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQLLKPTLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKESIEEPSAKINVLLQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNRGWAQLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVVKKIEKKNFPFERLYDLNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKVELTITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLITFFVPVFEPLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLDLQPLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSKCISIEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYENIPIRHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQLSAELQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWSKDSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEERNALLQLTDSQIADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQLEREEEVTGPVIAPLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATGAHNYTLYFMSDAYMGCDQEYKFSVDVKEAETDSDSD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.391
R work: 0.1795
R free: 0.253
Average B factor: 59.2729
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1M Hepes-NaOH, 0.1M MgCl2, 8% PEG 3350
Matthews coefficient: 2.44
Solvent content (%): 49.5
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: 2020-01-22
Crystal structure of the kinase domain of human c-KIT with a cyclic imidate inhibitor covalently bound to Cys788 (PDB entry 6XVB)
Macromolecule: Mast/stem cell growth factor receptor Kit,Mast/stem cell growth factor receptor Kit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 328 residues
Sequence: GSHMPMYEVQWKVVEESNGNNYSYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAQGLIKSDAAMTVAVKMLKPSAHSTEREALMSELKVLSYLGNHENIVNLLGACTHGGPTLVITEYCCYGDLLNFLRRKRDEFVPYKVAPEDLYKDFLTLEHLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGNITKICDFGLARDIKNDSNYVDKGNARLPVKWMAPESIFNSVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMSSPEYAPAEMYDIMKTCWDADPDKRPTFKQIVQDIEKQISESTNH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.192
R free: 0.223
Average B factor: 66.71
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.2
Crystallization temperature (K): 293
Crystal growth procedure: 9 % PEG8000, 18 % ethylene glycol, 10 % MORPHEUS halogens, 0.1 M Imidazole-MES buffer pH 6.2
Matthews coefficient: 2.42
Solvent content (%): 49.11
Ligand: ~{N}-(4,4-dimethyl-2-propyl-3,1-benzoxazin-6-yl)-2-[3-methoxy-5-(7-methoxyquinolin-4-yl)oxy-pyridin-2-yl]ethanamide (O2H)
Ligand formula: C31 H32 N4 O5
Ligand molecular weight: 540.61
Ligand SMILES: CCCC1=Nc2ccc(cc2C(O1)(C)C)NC(=O)Cc3c(cc(cn3)Oc4ccnc5c4ccc(c5)OC)OC
Ligand InChI: InChI=1S/C31H32N4O5/c1-6-7-30-35-24-11-8-19(14-23(24)31(2,3)40-30)34-29(36)17-26-28(38-5)16-21(18-33-26)39-27-12-13-32-25-15-20(37-4)9-10-22(25)27/h8-16,18H,6-7,17H2,1-5H3,(H,34,36)
Release date: 2020-05-27
DNA binding domain of human DNA Ligase IV mutant - A3V (PDB entry 7D9Y)
Macromolecule: DNA ligase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.5.1.1
Sequence length: 243 residues
Sequence: GSHMAVSQTSQTVASHVPFADLCSTLERIQKSKGRAEKIRHFREFLDSWRKFHDALHKNHKDVTDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPTGTHGDAGDFAMIAYFVLKPRCLQKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQLITQSSALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVCRQLHDPSVGLSDISI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.76
R work: 0.2343
R free: 0.2757
Average B factor: 66.7
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.125 M Tris pH 8.0, 20 % SOKALAN CP 42, 7.5% Methanol
Matthews coefficient: 3.26
Solvent content (%): 62.27
Release date: 2021-02-24
Crystal structure of human Urokinase-type plasminogen activator in complex with bicycle peptide inhibitor UK970 (PDB entry 7ZRT)
Macromolecule: Urokinase-type plasminogen activator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 253 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKEENGLAL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.208
R free: 0.229
Average B factor: 23.9
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.3
Crystallization temperature (K): 293
Crystal growth procedure: 7% PEG400, 50mM Citrato, 1.8 M (NH4)2SO4; 20% Ethylene glycol
Matthews coefficient: 2.01
Solvent content (%): 38.91
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: 2023-11-15
Crystal structure of human Fer SH2 domain bound to a phosphopeptide (DEpYENVD) (PDB entry 6KC4)
Macromolecule: Tyrosine-protein kinase Fer
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 102 residues
Sequence: GSKPLAEQDWYHGAIPRIEAQELLKKQGDFLVRESHGKPGEYVLSVYSDGQRRHFIIQYVDNMYRFEGTGFSNIPQLIDHHYTTKQVITKKSGVVLLNPIPK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.37
R work: 0.1646
R free: 0.1855
Average B factor: 20.8914
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 293
Crystal growth procedure: HEPES, sodium chloride, PEG 3350
Matthews coefficient: 2.15
Solvent content (%): 42.77
Release date: 2019-09-04
59th Ig domain of human obscurin (OBSCN Ig59) (PDB entry 5TZM)
Macromolecule: Obscurin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 100 residues
Sequence: RLEILELLKNAAVRAGAQACFTCTLSEAVPVGEASWYINGAAVQPDDSDWTVTADGSHHALLLRSAQPHHAGEVTFACRDAVASARLTVLGGLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.177
R work: 0.1642
R free: 0.1852
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 17% tacsimate, 0.1M HEPES pH 7.5, 4% PEG3350, 10 mg/mL C-terminal his-tagged Ig59
Matthews coefficient: 2.38
Solvent content (%): 48.4
Release date: 2017-11-08
CREBBP bromodomain in complex with Cpd6 (methyl 1H-indole-3-carboxylate) (PDB entry 6AXQ)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 114 residues
Sequence: AAFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1998
R free: 0.2161
Average B factor: 17.7644
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.2
Crystallization temperature (K): 289
Crystal growth procedure: 3.545 M Formate, 100 mM Tris-HCl pH 8.2, 10% glycerol
Matthews coefficient: 2.44
Solvent content (%): 49.67
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2018-02-21
The crystal structure of VASH1-SVBP complex (PDB entry 6OCF)
Macromolecule: Tubulinyl-Tyr carboxypeptidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.17
Sequence length: 248 residues
Sequence: VPFFVNRGGLPVDEATWERMWKHVAKIHPDGEKVAQRIRGATDLPKIPIPSVPTFQPSTPVPERLEAVQRYIRELQYNHTGTQFFEIKKSRPLTGLMDLAKEMTKEALPIKCLEAVILGIYLTNSMPTLERFPISFKTYFSGNYFRHIVLGVNFAGRYGALGMSRREDLMYKPPAFRTLSELVLDFEAAYGRCWHVLKKVKLGQSVSHDPHSVEQIEWKHSVLDVERLGRDDFRKELERHARDMRLKI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.102
R work: 0.1958
R free: 0.222
Average B factor: 41.7347
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M sodium citrate tribasic dihydrate, pH 5.0, and 18% (w/v) PEG20000
Matthews coefficient: 3.72
Solvent content (%): 66.96
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: 2019-06-26
Human methionine aminopeptidase type 1b (F309M mutant) in complex with ovalicin (PDB entry 5YKP)
Macromolecule: Methionine aminopeptidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 305 residues
Sequence: PYRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKLLSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCYPSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHGDLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHAQANGFSVVRSYCGHGIHKLMHTAPNVPHYAKNKAVGVMKSGHVFTIEPMICEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSARPHFMS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.68
R work: 0.1751
R free: 0.2117
Average B factor: 28.03
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M Hepes pH-6.0, 19% PEG MME 2000
Matthews coefficient: 2.56
Solvent content (%): 51.88
Ligand: POTASSIUM ION (K)
Ligand formula: K
Ligand molecular weight: 39.098
Ligand SMILES: [K+]
Ligand InChI: InChI=1S/K/q+1
Release date: 2018-10-17
Polymerase Beta Host Guest Complex Containing FapydG base paired with TMP (PDB entry 8VFJ)
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): 2.14
R work: 0.2107
R free: 0.2649
Average B factor: 33.44
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
Matthews coefficient: 2.62
Solvent content (%): 52.99
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2024-05-08
Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors (PDB entry 8DEA)
Macromolecule: Complement factor D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.46
Sequence length: 230 residues
Sequence: ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLASA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.214
R work: 0.225
R free: 0.2998
Average B factor: 33.495
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 293
Crystal growth procedure: peg4k 25% , 0.1M MES 5.8 buffer
Matthews coefficient: 2.13
Solvent content (%): 42.25
Ligand: 1-[(3-acetylphenyl)acetyl]-N-(6-bromopyridin-2-yl)-L-prolinamide (R7X)
Ligand formula: C20 H20 Br N3 O3
Ligand molecular weight: 430.295
Ligand SMILES: CC(=O)c1cccc(c1)CC(=O)N2CCCC2C(=O)Nc3cccc(n3)Br
Ligand InChI: InChI=1S/C20H20BrN3O3/c1-13(25)15-6-2-5-14(11-15)12-19(26)24-10-4-7-16(24)20(27)23-18-9-3-8-17(21)22-18/h2-3,5-6,8-9,11,16H,4,7,10,12H2,1H3,(H,22,23,27)/t16-/m0/s1
Release date: 2022-11-02
Crystal structure of CDK2 in complex with inhibitor ICEC0943 (PDB entry 5JQ8)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.19358
R free: 0.25976
Average B factor: 23.828
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M AMMONIUM ACETATE, PH 7.8, 6% PEG 3350
Matthews coefficient: 2.04
Solvent content (%): 39.62
Ligand: (3S,4S)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol (I73)
Ligand formula: C22 H30 N6 O
Ligand molecular weight: 394.513
Ligand SMILES: CC(C)c1cnn2c1nc(cc2NCc3ccccc3)NCC4CCNCC4O
Ligand InChI: InChI=1S/C22H30N6O/c1-15(2)18-13-26-28-21(25-11-16-6-4-3-5-7-16)10-20(27-22(18)28)24-12-17-8-9-23-14-19(17)29/h3-7,10,13,15,17,19,23,25,29H,8-9,11-12,14H2,1-2H3,(H,24,27)/t17-,19+/m0/s1
Release date: 2017-02-08
Structure of human DNA polymerase beta complexed with a nicked DNA containing a AC at N-1 position and GC at N position (PDB entry 4PH5)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACGACGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.191
R free: 0.2612
Average B factor: 30.31
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 14%?23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.28
Solvent content (%): 46.16
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: 2015-05-06
PP1 H66K in complex with Microcystin LR (PDB entry 6OBQ)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 299 residues
Sequence: GHMGSLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIKGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.2302
R free: 0.2602
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG6000, 1 M lithium chloride, 0.1 M MES
Matthews coefficient: 2.31
Solvent content (%): 46.86
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: 2019-09-18
Structure of AKR1C3 in complex with a bile acid fused tetrazole inhibitor (PDB entry 8BBS)
Macromolecule: Aldo-keto reductase family 1 member C3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 326 residues
Sequence: GSHMDSKHQCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKKAQLDYVDLYLIHSPMSLKPGEELSPTDENGKVIFDIVDLCTTWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHYFNSDSFASHPNYPYSDEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1546
R free: 0.1775
Average B factor: 17.31
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 295
Crystal growth procedure: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD and 0.02 M each of DL-glutamic acid monohydrate, DL-alanine, glycine, DL-lysine monohydrochloride, and DL-serine; in 0.1 M bicine/Trizma base, pH 8.5
Matthews coefficient: 2.02
Solvent content (%): 39.23
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2023-03-08
Human DNA polymerase theta in complex with allosteric inhibitor (PDB entry 8E24)
Macromolecule: DNA polymerase theta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 668 residues
Sequence: GASSSSESLSIIDVASDQNLFQTFIKEWRCKKRFSISLACEKIRSLTSSKTGFPIKGCDDTLVVGLAVCWGGRDAYYFSLQKESLDPSLTLKDRMWYLQSCLRKESDKECSVVIYDFIQSYKILLLSCGISLEQSYEDPKVACWLLDPDSQEPTLHSIVTSFLPHELPLLEGMETSQGIQSLGLNAGSEHSGRYRASVESILIFNSMNQLNSLLQKENLQDVFRKVEMPSQYCLALLELNGIGFSTAECESQKHIMQAKLDAIETQAYQLAGHSFSFTSSDDIAEVLFLELKLPPNRELGRQFSTSKDVLNKLKALHPLPGLILEWRRITNAITKVVFPLQREKCLNPFLGMERIYPVSQSHTATGRITFTEPNIQNVPRDFEIKMPTLADRGMPFSISMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLETFHSTFKSHGHREGMLQSDQTGGMFCPIRGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMESAVKLSVKLKVKVKIGASWGELKDFDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.34
R work: 0.2314
R free: 0.2662
Average B factor: 79.29
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 16% PEG 3350, 0.2M diammonium tartrate, 2% glycerol
Matthews coefficient: 2.88
Solvent content (%): 62.39
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: 2022-09-28