satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of Glucokinase in complex with compound 6 (PDB entry 6E0E)
Macromolecule: Glucokinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.2
Sequence length: 448 residues
Sequence: TLVEQILAEFQLQEEDLKKVMRRMQKEMDRGLRLETHEEASVKMLPTYVRSTPEGSEVGDFLSLDLGGTNFRVMLVKVGEGEEGQWSVKTKHQMYSIPEDAMTGTAEMLFDYISECISDFLDKHQMKHKKLPLGFTFSFPVRHEDIDKGILLNWTKGFKASGAEGNNVVGLLRDAIKRRGDFEMDVVAMVNDTVATMISCYYEDHQCEVGMIVGTGCNACYMEEMQNVELVEGDEGRMCVNTEWGAFGDSGELDEFLLEYDRLVDESSANPGQQLYEKLIGGKYMGELVRLVLLRLVDENLLFHGEASEQLRTRGAFETRFVSQVESDTGDRKQIYNILSTLGLRPSTTDCDIVRRACESVSTRAAHMCSAGLAGVINRMRESRSEDVMRITVGVDGSVYKLHPSFKERFHASVRRLTPSCEITFIESEEGSGRGAALVSAVACKKAC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.20284
R free: 0.27659
Average B factor: 55.307
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Hepes pH7.0, 27% PEG1500
Matthews coefficient: 2.91
Solvent content (%): 57.74
Ligand: alpha-D-glucopyranose (GLC)
Ligand formula: C6 H12 O6
Ligand molecular weight: 180.156
Ligand SMILES: C(C1C(C(C(C(O1)O)O)O)O)O
Ligand InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
Release date: 2019-07-10
DNA Polymerase Mu Product Complex, Mn2+ (15 min) (PDB entry 5TYX)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.948
R work: 0.1854
R free: 0.2161
Average B factor: 30.734
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.68
Solvent content (%): 54.05
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: 2017-08-30
Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 4) (PDB entry 7MOS)
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): 1.704
R work: 0.1827
R free: 0.2084
Average B factor: 27.87
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 (%): 50.26
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
HRas G12V in complex with GDP (PDB entry 7TAM)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 166 residues
Sequence: MTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.1741
R free: 0.201
Average B factor: 31.8271
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295.15
Crystal growth procedure: 29% PEG 3350, 0.2 M calcium chloride, 0.1 M TRIS hydrochloride
Matthews coefficient: 2.63
Solvent content (%): 53.3
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: 2022-12-28
The X-ray co-crystal structure of human CDK6 and Ribociclib. (PDB entry 5L2T)
Macromolecule: Cyclin-dependent kinase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 307 residues
Sequence: MEKDGLCRADQQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVQTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDRETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLDFLHSHRVVHRDLKPQNILVTSSGQIKLADFGLARIYSFQMALTSVVVTLWYRAPEVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILDVIGLPGEEDWPRDVALPRQAFHSKSAQPIEKFVTDIDELGKDLLLKCLTFNPAKRISAYSALSHPYFQHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.37
R work: 0.2117
R free: 0.2576
Average B factor: 68.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 286.15
Crystal growth procedure: 1:1 (protein to well buffer) with well buffer containing:  0.1 M MES pH 6.0, 70 - 80 mM NH4NO3, 10 - 15% polyethyleneglycol 3350
Matthews coefficient: 2.26
Solvent content (%): 45.56
Ligand: 7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide (6ZZ)
Ligand formula: C23 H30 N8 O
Ligand molecular weight: 434.537
Ligand SMILES: CN(C)C(=O)c1cc2cnc(nc2n1C3CCCC3)Nc4ccc(cn4)N5CCNCC5
Ligand InChI: InChI=1S/C23H30N8O/c1-29(2)22(32)19-13-16-14-26-23(28-21(16)31(19)17-5-3-4-6-17)27-20-8-7-18(15-25-20)30-11-9-24-10-12-30/h7-8,13-15,17,24H,3-6,9-12H2,1-2H3,(H,25,26,27,28)
Release date: 2016-08-24
KRAS 1-169 G12C Mutant at 293k (PDB entry 8TY2)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 169 residues
Sequence: MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.1805
R free: 0.208
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 200mM Na Acetate pH 3.6
100mM Tris pH 8.5
20% PEG 3350
1mM DTT
Matthews coefficient: 1.98
Solvent content (%): 37.76
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: 2024-08-28
FGFR2 kinase domain (residues 461-763) in complex with 38. (PDB entry 7OZY)
Macromolecule: Fibroblast growth factor receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 303 residues
Sequence: GSHMEYELPEDPKWEFPRDKLTLGKPLGEGCFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPGMEYSYDINRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKKTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.2403
R free: 0.2959
Average B factor: 50.923
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.6
Crystallization temperature (K): 291
Crystal growth procedure: 25% w/v PEG 3350, 0.1 M ammonium sulfate, 0.1 M HEPES
Matthews coefficient: 2.73
Solvent content (%): 54.98
Ligand: 4-[3-(4-piperazin-4-ium-1-ylphenyl)-1H-indazol-6-yl]phenol (47I)
Ligand formula: C23 H23 N4 O
Ligand molecular weight: 371.455
Ligand SMILES: c1cc(ccc1c2c3ccc(cc3[nH]n2)c4ccc(cc4)O)N5CC[NH2+]CC5
Ligand InChI: InChI=1S/C23H22N4O/c28-20-8-3-16(4-9-20)18-5-10-21-22(15-18)25-26-23(21)17-1-6-19(7-2-17)27-13-11-24-12-14-27/h1-10,15,24,28H,11-14H2,(H,25,26)/p+1
Release date: 2021-12-01
Crystal Structure of EGFR-T790M/C797S in Complex with Covalent Pyrrolopyrimidine 19g (PDB entry 6S89)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 333 residues
Sequence: GSHMASGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGSLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.701
R work: 0.1882
R free: 0.2337
Average B factor: 80.0011
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.35 K-Na-tartrate, 100 mM Na-MES (pH 6.5), 2 % 1,3-Propanediol, 5.5 mg/ml EGFR T790M/C797 (in 100 mM NaCl, 25mM Tris-HCl, 10 % Glycerol, 1mM TCEP, pH 8.0), 1 ul reservoir + 1 ul protein solution
Matthews coefficient: 3.3
Solvent content (%): 62.67
Ligand: ~{N}-[3-[6-[4-(4-methylpiperazin-1-yl)phenyl]-4-propan-2-yloxy-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]phenyl]propanamide (L0Q)
Ligand formula: C29 H34 N6 O2
Ligand molecular weight: 498.619
Ligand SMILES: CCC(=O)Nc1cccc(c1)c2c3c([nH]c2c4ccc(cc4)N5CCN(CC5)C)ncnc3OC(C)C
Ligand InChI: InChI=1S/C29H34N6O2/c1-5-24(36)32-22-8-6-7-21(17-22)25-26-28(30-18-31-29(26)37-19(2)3)33-27(25)20-9-11-23(12-10-20)35-15-13-34(4)14-16-35/h6-12,17-19H,5,13-16H2,1-4H3,(H,32,36)(H,30,31,33)
Release date: 2019-10-16
Crystal structure of human carbonic anhydrase VII (hCA VII) in complex with a 4-(4-aroylpiperazine-1-carbonyl)benzenesulfonamide derivative. (PDB entry 7NC4)
Macromolecule: Carbonic anhydrase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 274 residues
Sequence: MGMTGHHGWGYGQDDGPSHWHKLYPIAQGDRQSPINIISSQAVYSPSLQPLELSYEACMSLSITNNGHSVQVDFNDSDDRTVVTGGPLEGPYRLKQFHFHWGKKHDVGSEHTVDGKSFPSELHLVHWNAKKYSTFGEAASAPDGLAVVGVFLETGDEHPSMNRLTDALYMVRFKGTKAQFSCFNPKSLLPASRHYWTYPGSLTTPPLSESVTWIVLREPISISERQMGKFRSLLFTSEDDERIHMVNNFRPPQPLKGRVVKASFRALEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1959
R free: 0.214
Average B factor: 24.712
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 18% PEG 3350, 0.2 M Sodium Acetate, 0.1 M Tris-HCl pH 8.5
Matthews coefficient: 2.1
Solvent content (%): 41.55
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
HDM2 (17-111, WILD TYPE) COMPLEXED WITH NVP-HDM201 AT 1.56A (PDB entry 5OC8)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 96 residues
Sequence: GSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.237
R free: 0.2603
Average B factor: 24.069
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 298
Crystal growth procedure: 3M AmSO4, 0.1M citrate
Matthews coefficient: 2.16
Solvent content (%): 43.04
Ligand: (4~{S})-5-(5-chloranyl-1-methyl-2-oxidanylidene-pyridin-3-yl)-4-(4-chlorophenyl)-2-(2,4-dimethoxypyrimidin-5-yl)-3-propan-2-yl-4~{H}-pyrrolo[3,4-d]imidazol-6-one (9QW)
Ligand formula: C26 H24 Cl2 N6 O4
Ligand molecular weight: 555.413
Ligand SMILES: CC(C)n1c2c(nc1c3cnc(nc3OC)OC)C(=O)N(C2c4ccc(cc4)Cl)C5=CC(=CN(C5=O)C)Cl
Ligand InChI: InChI=1S/C26H24Cl2N6O4/c1-13(2)33-21-19(30-22(33)17-11-29-26(38-5)31-23(17)37-4)25(36)34(18-10-16(28)12-32(3)24(18)35)20(21)14-6-8-15(27)9-7-14/h6-13,20H,1-5H3/t20-/m0/s1
Release date: 2018-08-22
Crystal structure of human beta2 adrenergic receptor bound to salmeterol and Nb71 (PDB entry 6MXT)
Macromolecule: Endolysin, Beta-2 adrenergic receptor chimera
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 472 residues
Sequence: GNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYAADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILTKTWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLQKIDKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCLRRSSLKAYGNGYSSNGNTGEQSG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95934213525
R work: 0.204625198648
R free: 0.24486451981
Average B factor: 53.7137652891
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 7.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 31-34% PEG400, 100 mM HEPES, pH 7.5, 1% 1,2,3-heptanetriol
Matthews coefficient: 3.8
Solvent content (%): 67.64
Ligand: salmeterol (K5Y)
Ligand formula: C25 H37 N O4
Ligand molecular weight: 415.566
Ligand SMILES: c1ccc(cc1)CCCCOCCCCCCNCC(c2ccc(c(c2)CO)O)O
Ligand InChI: InChI=1S/C25H37NO4/c27-20-23-18-22(13-14-24(23)28)25(29)19-26-15-7-1-2-8-16-30-17-9-6-12-21-10-4-3-5-11-21/h3-5,10-11,13-14,18,25-29H,1-2,6-9,12,15-17,19-20H2/t25-/m0/s1
Release date: 2018-11-14
Crystal structure of AKR1C1 in complex with DFV (PDB entry 8JP2)
Macromolecule: Aldo-keto reductase family 1 member C1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 323 residues
Sequence: MDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1965
R free: 0.2491
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 298
Crystal growth procedure: 23-27% (w/v) PEG 4000, 100 mM Hepes , 10 mM CaCl2 and 0.4 M NaCl
Matthews coefficient: 2.2
Solvent content (%): 44.19
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: 2024-04-24
HIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND L-GLUTAMATE TENOFOVIR (PDB entry 7AIG)
Macromolecule: Gag-Pol polyprotein
Type: Protein, polypeptide(L)
Source organism: Human immunodeficiency virus type 1 BH10
EC number: 3.4.23.16
Sequence length: 556 residues
Sequence: MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDICKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTNSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.2132
R free: 0.257
Average B factor: 106.17
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 16-19.5% v/v PEG Smear Broad, 
0.2 M (NH4)2SO4, 
0.1 M Tris-HCl
Matthews coefficient: 3.19
Solvent content (%): 61.5
Ligand: L-Glutamate Tenofovir (RE5)
Ligand formula: C14 H21 N6 O7 P
Ligand molecular weight: 416.326
Ligand SMILES: CC(Cn1cnc2c1ncnc2N)OCP(=O)(NC(CCC(=O)O)C(=O)O)O
Ligand InChI: InChI=1S/C14H21N6O7P/c1-8(4-20-6-18-11-12(15)16-5-17-13(11)20)27-7-28(25,26)19-9(14(23)24)2-3-10(21)22/h5-6,8-9H,2-4,7H2,1H3,(H,21,22)(H,23,24)(H2,15,16,17)(H2,19,25,26)/t8-,9+/m1/s1
Release date: 2021-01-13
Pyridopyrimidinone Derivatives as Potent and Selective c-Jun N-Terminal Kinase (JNK) inhibitors (PDB entry 4Y5H)
Macromolecule: Mitogen-activated protein kinase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 366 residues
Sequence: MAMSKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.055
R work: 0.2362
R free: 0.2852
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG 3350, ammonium tartrate
Matthews coefficient: 2.46
Solvent content (%): 49.99
Ligand: 1-(trans-4-{[7-oxo-8-(propan-2-yl)-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl]amino}cyclohexyl)-3-propan-2-ylurea (519)
Ligand formula: C20 H30 N6 O2
Ligand molecular weight: 386.491
Ligand SMILES: CC(C)NC(=O)NC1CCC(CC1)Nc2ncc3c(n2)N(C(=O)C=C3)C(C)C
Ligand InChI: InChI=1S/C20H30N6O2/c1-12(2)22-20(28)24-16-8-6-15(7-9-16)23-19-21-11-14-5-10-17(27)26(13(3)4)18(14)25-19/h5,10-13,15-16H,6-9H2,1-4H3,(H,21,23,25)(H2,22,24,28)/t15-,16-
Release date: 2015-05-06
Crystal structure of the N-terminal domain single mutant (S92E) of the human mitochondrial calcium uniporter fused with T4 lysozyme (PDB entry 6JG0)
Macromolecule: Endolysin,Calcium uniporter protein
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 262 residues
Sequence: MNIFEMLRIDEGLRLKIYKNTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYGSVTVVYQNGLPVISVRLPERRERCQFTLKPISDSVGVFLRQLQEEDRGIDRVAIYSPDGVRVAASTGIDLLLLDDFKLVINDLTYHVRPPKRLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.18796
R free: 0.25903
Average B factor: 51.417
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350, 5% glycerol, 0.3 M (NH4)2SO4, and 0.1 M Bis-Tris-HCl (pH 5.5)
Matthews coefficient: 2.86
Solvent content (%): 56.92
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: 2020-02-19
Crystal structure of human SHIP2 Phosphatase-C2 double mutant F593D/L597D (PDB entry 5OKO)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 461 residues
Sequence: GPEPDMISVFIGTWNMGSVPPPKNVTSWFTSKGLGKTLDEVTVTIPHDIYVFGTQENSVGDREWLDLLRGGLKELTDLDYRPIAMQSLWNIKVAVLVKPEHENRISHVSTSSVKTGIANTLGNKGAVGVSFMFNGTSFGFVNCHLTSGNEKTARRNQNYLDILRLLSLGDRQLNADDISDRFTHLFWFGDLNYRLDMDIQEILNYISRKEFEPLLRVDQLNLEREKHKVFLRFSEEEISFPPTYRYERGSRDTYAWHKQKPTGVRTNVPSWCDRILWKSYPETHIICNSYGCTDDIVTSDHSPVFGTFEVGVTSQFISKKGLSKTSDQAYIEFESIEAIVKTASRTKFFIEFYSTCLEEYKKSFENDAQSSDNINFLKVQWSSRQLPTLKPILADIEYLQDQHLLLTVKSMDGYESYGECVVALKSMIGSTAQQFLTFLSHRGEETGNIRGSMKVRVPTER
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.18957
R free: 0.22872
Average B factor: 26.809
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M PCB (sodium propionate, sodium cacodylate, and BIS-TRIS propane; 2:1:2 molar ratio) pH 7, 25% PEG 1500
Matthews coefficient: 2.21
Solvent content (%): 44.35
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: 2017-08-23
Crystal structure of hPin1 WW domain (5-21) fused with maltose-binding protein (PDB entry 5BMY)
Macromolecule: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 389 residues
Sequence: MEKLPPGWEKRMSRSSGRGSGMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.001
R work: 0.1537
R free: 0.1937
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 2.1 M DL-malic acid
Matthews coefficient: 2.2
Solvent content (%): 44.02
Release date: 2016-10-26
Protein Kinase A in complex with an Inhibitor (PDB entry 4UJ2)
Macromolecule: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.11
Sequence length: 351 residues
Sequence: MGNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.019
R work: 0.1615
R free: 0.2092
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 10MG/ML PROTEIN, 25MM BISTRIS/MES PH6.9, 50MM KCL, 1.5MM OCTANOYL-N-METHYLGLUCAMIDE, 1MM PROTEIN KINASE INHIBITOR PEPTIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
Matthews coefficient: 2.47
Solvent content (%): 50.15
Ligand: 7-[(3S,4R)-4-(3-iodanylphenyl)carbonylpyrrolidin-3-yl]-3H-quinazolin-4-one (NVV)
Ligand formula: C19 H16 I N3 O2
Ligand molecular weight: 445.254
Ligand SMILES: c1cc(cc(c1)I)C(=O)C2CNCC2c3ccc4c(c3)N=CNC4=O
Ligand InChI: InChI=1S/C19H16IN3O2/c20-13-3-1-2-12(6-13)18(24)16-9-21-8-15(16)11-4-5-14-17(7-11)22-10-23-19(14)25/h1-7,10,15-16,21H,8-9H2,(H,22,23,25)/t15-,16+/m1/s1
Release date: 2016-04-13