satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of the USP15 deubiquitinase domain in complex with an affinity-matured inhibitory Ubv (PDB entry 6ML1)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15,Ubiquitin carboxyl-terminal hydrolase 15
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 349 residues
Sequence: SGAAADYSEPGRNNEQPGLCGLSNLGNTCFMNSAIQCLSNTPPLTEYFLNDKYQEELNFDNPLGMRGEIAKSYAELIKQMWSGKFSYVTPRAFKTQVGRFAPQFSGYQQQDCQELLAFLLDGLHEDLNRIRKKPYIQLKDADGRPDKVVAEEAWENHLKRNDSIIVDIFHGLFKSTLVCPECAKISVTFDPFCYLTLPLPMPKKPFVKLKDCIELFTTKEKLGAEDPWYCPNCKEHQQATKKLDLWSLPPVLVVHLKRFSYSRYMRDKLDTLVDFPINDLDMSGCRYNLIAVSNHYGGMGGGHYTAFAKNKDDGKWYYFDDSSVSTASEDQIVSKAAYVLFYQRQDSSG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1894
R free: 0.2195
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 16% PEG3350, 100 mM MES 6.0, 250 mM CaCl2, cryoprotected with 18% PEG3350, 200 mM CaCl2, 100 mM MES pH 6.5 and 25% glycerol
Matthews coefficient: 2.37
Solvent content (%): 48.15
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2019-01-23
AMP-activated protein kinase bound to pharmacological activator R739 (PDB entry 6C9G)
Macromolecule: 5'-AMP-activated protein kinase subunit beta-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 204 residues
Sequence: MEVNDKAPAQARPTVFRWTGGGKEVYLSGSFNNWSKLPLTRDHNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVKKTDFEVFDALMVDSQKCSDVSELSSSPPGPYHQEPYVCKPEERFRAPPILPPHLLQVILNKDTGISCDPALLPEPNHVMLNHLYALSIKDGVMVLSATHRYKKKYVTTLLYKPI
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2023
R free: 0.2401
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M tri-sodium acetate pH 5.6, 0.2 M ammonium acetate, 15% w/v PEG 4000
Matthews coefficient: 3.74
Solvent content (%): 67.15
Ligand: 5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide (R93)
Ligand formula: C27 H20 Cl N3 O4
Ligand molecular weight: 485.918
Ligand SMILES: Cc1ccc(cc1C(=O)NO)Oc2[nH]c3cc(c(cc3n2)c4ccc(cc4)c5ccccc5O)Cl
Ligand InChI: InChI=1S/C27H20ClN3O4/c1-15-6-11-18(12-20(15)26(33)31-34)35-27-29-23-13-21(22(28)14-24(23)30-27)17-9-7-16(8-10-17)19-4-2-3-5-25(19)32/h2-14,32,34H,1H3,(H,29,30)(H,31,33)
Release date: 2018-11-28
DYRK1A in complex with XMD8-62e (PDB entry 6EIP)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 368 residues
Sequence: GASDSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADEGTNTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.56
R work: 0.24145
R free: 0.2662
Average B factor: 52.174
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M KSCN; 0.05M LiCl; 10% PEG 3350, pH 6.8
Matthews coefficient: 2.61
Solvent content (%): 52.88
Ligand: 4-[[(3~{R},7~{S})-2-cyclopentyl-9-methyl-8-oxidanylidene-2,9,12,14-tetrazatricyclo[8.4.0.0^{3,7}]tetradeca-1(14),10,12-trien-13-yl]amino]benzamide (B7B)
Ligand formula: C23 H28 N6 O2
Ligand molecular weight: 420.507
Ligand SMILES: CN1c2cnc(nc2N(C3CCCC3C1=O)C4CCCC4)Nc5ccc(cc5)C(=O)N
Ligand InChI: InChI=1S/C23H28N6O2/c1-28-19-13-25-23(26-15-11-9-14(10-12-15)20(24)30)27-21(19)29(16-5-2-3-6-16)18-8-4-7-17(18)22(28)31/h9-13,16-18H,2-8H2,1H3,(H2,24,30)(H,25,26,27)/t17-,18+/m0/s1
Release date: 2018-08-29
Crystal structure of tRNA 2'-phosphotransferase from Homo sapiens (PDB entry 7YW3)
Macromolecule: tRNA 2'-phosphotransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.160
Sequence length: 253 residues
Sequence: MNFSGGGRQEAAGSRGRRAPRPREQDRDVQLSKALSYALRHGALKLGLPMGADGFVPLGTLLQLPQFRGFSAEDVQRVVDTNRKQRFALQLGDPSTGLLIRANQGHSLQVPKLELMPLETPQALPPMLVHGTFWKHWPSILLKGLSCQGRTHIHLAPGLPGDPGIISGMRSHCEIAVFIDGPLALADGIPFFRSANGVILTPGNTDGFLLPKYFKEALQLRPTRKPLSLAGDEETECQSSPKHSSRERRRIQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.252
R free: 0.2949
Average B factor: 48.2627
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M Tris pH 8.0
28 % PEG4000
Matthews coefficient: 2.07
Solvent content (%): 40.59
Ligand: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate (HQG)
Ligand formula: C15 H24 N5 O17 P3
Ligand molecular weight: 639.296
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)OP(=O)(O)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H24N5O17P3/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(34-14)1-32-39(28,29)37-40(30,31)33-2-6-9(22)11(24)15(35-6)36-38(25,26)27/h3-6,8-11,14-15,21-24H,1-2H2,(H,28,29)(H,30,31)(H2,16,17,18)(H2,25,26,27)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1
Release date: 2023-07-26
Structure of human DNA polymerase beta Host-Guest complexed with CBZ-platinated N7-G (PDB entry 5HHI)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 329 residues
Sequence: PQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.517
R work: 0.2223
R free: 0.2792
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 14 to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Matthews coefficient: 2.4
Solvent content (%): 48.66
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-01-18
complex of Dot1l with SS148 (PDB entry 5JUW)
Macromolecule: Histone-lysine N-methyltransferase, H3 lysine-79 specific
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 421 residues
Sequence: GMGEKLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKNPKLREEQEAARRRQQRESKSNAATPTKGPEGKVAGPADAPMDSGAEEEKAGAATVKKPSPSKARKKKLNKKGRKMAGRKRGRPKKMNTA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.1886
R free: 0.2153
Average B factor: 46.253
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 291
Crystal growth procedure: 1.5 M ammonium sulfate, 0.1 M ammonium acetate
Matthews coefficient: 3.58
Solvent content (%): 65.68
Ligand: UNKNOWN ATOM OR ION (UNX)
Ligand formula: X
Ligand SMILES: *
Release date: 2016-06-22
Benzensulfonamides bearing spyrohydantoin moieties act as potent inhibitors of human carbonic anhydrases II and VII and show neuropathic pain attenuating effects (PDB entry 6OE0)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.2138
R free: 0.23855
Average B factor: 9.326
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 200 nL 7 mg/mL protein + 200 nL reservoir (50 mM Tris, pH 8.0-8.2, 2.5-2.8 M ammonium sulfate)
Matthews coefficient: 2.1
Solvent content (%): 41.31
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: 2019-06-12
Crystal structure of human SUMO E1 UFD domain in complex with Ubc9 in a P422 space group. (PDB entry 5FQ2)
Macromolecule: SUMO-CONJUGATING ENZYME UBC9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 161 residues
Sequence: GSHMSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.201
R work: 0.2293
R free: 0.2489
Matthews coefficient: 4.65
Solvent content (%): 75.53
Release date: 2016-11-16
Crystal structure of human carbonic anhydrase I in complex with the 4-[(3S)-3 benzyl-4-(4-sulfamoylbenzoyl)piperazine -1-carbonyl]benzene-1-sulfonamide inhibitor (PDB entry 6EX1)
Macromolecule: Carbonic anhydrase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 261 residues
Sequence: MASPDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.21398
R free: 0.2437
Average B factor: 37.328
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 296
Crystal growth procedure: 28% PEG4000, 0.2 M Sodium acetate, Tris 100 mM
Matthews coefficient: 2.33
Solvent content (%): 47.12
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: 2018-10-10
Structure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate Rab1 (PDB entry 8ALK)
Macromolecule: Phosphocholine hydrolase Lem3
Type: Protein, polypeptide(L)
Source organism: Legionella pneumophila
EC number: 3.1.3
Sequence length: 469 residues
Sequence: GHMDKIITGKKIIFSQSVAKDQTKNLSSFLSERFYSVNQSHNHSIIIGSSLSHQENDIEHDTILDTSGVLVTTDTNGIVNGARVAITDGLGGGNGDQEEDDEIYRVSHSSCENFLNSDQNIDTTLSLITQPKASDKKQTAPKTLQHTEASMAAFIYQNHPGKGYIGEFANIGDGLIIILDKRFKIKHMVSASHIYRGFGTWTPPSLQALATTANKDALLVRQTLKLAEGDIIISMTDGVWGELKTSLIAQTNDRRDIGVDKEYFKTLFDELTDAPYPSSFDIARIITQRAMSRSLERRKTLIKLINEIEQQHFHEKSVKTINEVLEYFIKTGHVETAQTLKAILFEDGLSDGITYFENIEIPLEMVMHDLKSRCVGDCSTINVTRIPYHLDELIRGFINYPEKHQILAPLFKARVKSEADLEEAFHRLSLEMVQPEIESPISETHFERAFKKETLDKTQAVLTHYFRIS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1813
R free: 0.2275
Average B factor: 59.06
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: MES 0.1M pH 5, PEG6000 5%
Matthews coefficient: 2.23
Solvent content (%): 44.97
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2023-04-12
PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-359-835 (PDB entry 5QQK)
Macromolecule: Ras-related C3 botulinum toxin substrate 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 178 residues
Sequence: SMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.1999
R free: 0.2656
Average B factor: 44.67
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1M bis-tris pH 5.5 24% PEG 3350
Matthews coefficient: 2.35
Solvent content (%): 47.74
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: 2019-12-18
Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain (PDB entry 5WBN)
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): 1.64
R work: 0.1319
R free: 0.1675
Average B factor: 9.104
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 291
Crystal growth procedure: 2M Na-formate, 0.2M 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: 2017-08-02
FXIIIa in complex with the inhibitor ZED1630 (PDB entry 5MHM)
Macromolecule: Coagulation factor XIII A chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.13
Sequence length: 738 residues
Sequence: MHHHHHHSETSRTAFGGRRAVPPNNSNAAEDDLPTVELQGVVPRGVNLQEFLNVTSVHLFKERWDTNKVDHHTDKYENNKLIVRRGQSFYVQIDFSRPYDPRRDLFRVEYVIGRYPQENKGTYIPVPIVSELQSGKWGAKIVMREDRSVRLSIQSSPKCIVGKFRMYVAVWTPYGVLRTSRNPETDTYILFNPWCEDDAVYLDNEKEREEYVLNDIGVIFYGEVNDIKTRSWSYGQFEDGILDTCLYVMDRAQMDLSGRGNPIKVSRVGSAMVNAKDDEGVLVGSWDNIYAYGVPPSAWTGSVDILLEYRSSENPVRYGQCWVFAGVFNTFLRCLGIPARIVTNYFSAHDNDANLQMDIFLEEDGNVNSKLTKDSVWNYHCWNEAWMTRPDLPVGFGGWQAVDSTPQENSDGMYRCGPASVQAIKHGHVCFQFDAPFVFAEVNSDLIYITAKKDGTHVVENVDATHIGKLIVTKQIGGDGMMDITDTYKFQEGQEEERLALETALMYGAKKPLNTEGVMKSRSNVDMDFEVENAVLGKDFKLSITFRNNSHNRYTITAYLSANITFYTGVPKAEFKKETFDVTLEPLSFKKEAVLIQAGEYMGQLLEQASLHFFVTARINETRDVLAKQKSTVLTIPEIIIKVRGTQVVGSDMTVIVEFTNPLKETLRNVWVHLDGPGVTRPMKKMFREIRPNSTVQWEEVCRPWVSGHRKLIASMSSDSLRHVYGELDVQIQRRPSM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.17
R free: 0.213
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 170 mM ammonium sulfate, 85 mM sodium cacodylate, 25.5 % PEG8000, 15 % glycerol
Matthews coefficient: 2.7
Solvent content (%): 54.4
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: 2017-12-20
Crystal Structure of human phosphodiesterase 10 in complex with 4-(2-chloroquinazolin-4-yl)morpholine (PDB entry 5SJ6)
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): 2.15
R work: 0.182
R free: 0.2347
Average B factor: 42.967
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: 2.59
Solvent content (%): 52.54
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
X-RAY STRUCTURE OF MPS1 IN COMPLEX WITH COMPOUND 79 (PDB entry 6TND)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 294 residues
Sequence: GSNECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58
R work: 0.1865
R free: 0.2494
Average B factor: 60.329
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 10% PEG 3350, 180mM Magnesium formate, 25% glycerol
Matthews coefficient: 3.65
Solvent content (%): 66.33
Ligand: BAY 1217389 (8RH)
Ligand formula: C27 H24 F5 N5 O3
Ligand molecular weight: 561.503
Ligand SMILES: Cc1cc(ccc1C(=O)NC2CC2)c3cnc4n3nc(cc4NCCC(F)(F)F)Oc5ccc(c(c5F)F)OC
Ligand InChI: InChI=1S/C27H24F5N5O3/c1-14-11-15(3-6-17(14)26(38)35-16-4-5-16)19-13-34-25-18(33-10-9-27(30,31)32)12-22(36-37(19)25)40-21-8-7-20(39-2)23(28)24(21)29/h3,6-8,11-13,16,33H,4-5,9-10H2,1-2H3,(H,35,38)
Release date: 2020-05-13
Crystal Structure of CK2alpha with CAM187 bound (PDB entry 6GIH)
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): 1.96
R work: 0.18
R free: 0.215
Average B factor: 23.45
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: 2.04
Solvent content (%): 39.68
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: 2018-05-23
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5- phosphonodifluoroacetamide inositol pentakisphosphate (5-PCF2Am-InsP5), an analogue of 5-InsP7 (PDB entry 8G9D)
Macromolecule: Diphosphoinositol polyphosphate phosphohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.52
Sequence length: 172 residues
Sequence: MMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYSANNGTPVVATTYSVSAQSSMSGIR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.19118
R free: 0.22527
Average B factor: 15.776
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 10% (w/v) PEG 8000, 10% (v/v) isopropanol, 200 mM Li2SO4, 75 mM NaAc, pH 5.5 and 25 mM HEPES, pH 7.0 and soaking in solution 200mM LiCl, 20% PEG8000, 20% isopropanol, 100mM HEPES 7.0, 20mM MgCl2 in the present of 2mM 5-PCF2Am-IP7
Matthews coefficient: 2.22
Solvent content (%): 44.57
Ligand: (1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic acid (KDJ)
Ligand formula: C8 H19 F2 N O24 P6
Ligand molecular weight: 737.068
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)NC(=O)C(F)(F)P(=O)(O)O
Ligand InChI: InChI=1S/C8H19F2NO24P6/c9-8(10,36(13,14)15)7(12)11-1-2(31-37(16,17)18)4(33-39(22,23)24)6(35-41(28,29)30)5(34-40(25,26)27)3(1)32-38(19,20)21/h1-6H,(H,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)(H2,25,26,27)(H2,28,29,30)/t1-,2-,3+,4+,5-,6+
Release date: 2024-01-03
Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3543105A (PDB entry 7SFD)
Macromolecule: DNA (cytosine-5)-methyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.37
Sequence length: 874 residues
Sequence: HMNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKFKFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLSSPVKRPRKEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSPGNKGKGKGKGKGKPKSQACEPSEPEIEIKLPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACDPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.185
R free: 0.2159
Average B factor: 60.91
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.1
Crystallization temperature (K): 292
Crystal growth procedure: 14-18% polyethylene glycol (PEG) 3350,  0.1 M citric acid (pH 5.1)
Matthews coefficient: 2.79
Solvent content (%): 55.85
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2022-03-30