satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of PLEKHM1 RUN domain in complex with GTP-bound Arl8b(Q75L) (PDB entry 8JC5)
Macromolecule: ADP-ribosylation factor-like protein 8B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 169 residues
Sequence: KEEMELTLVGLQYSGKTTFVNVIASGQFSEDMIPTVGFNMRKVTKGNVTIKIWDIGGLPRFRSMWERYCRGVNAIVYMIDAADREKIEASRNELHNLLDKPQLQGIPVLVLGNKRDLPNALDEKQLIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHSKSRRS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.01
R work: 0.1669
R free: 0.2009
Average B factor: 51.15
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.2 M Lithium chloride, 0.1 M TRIS pH=7.6, 18% (w/v) PEG 8000
Matthews coefficient: 3.04
Solvent content (%): 59.48
Ligand: GUANOSINE-5'-TRIPHOSPHATE (GTP)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2024-03-27
ATAD2 bromodomain in complex with "oncohistone" mutation H4S1CK5ac (res 1-15) ligand (PDB entry 8SDO)
Macromolecule: Histone H4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 15 residues
Sequence: CGRGKGGKGLGKGGA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.01
R work: 0.2007
R free: 0.2305
Average B factor: 56.87
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2.4 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 6.4
Matthews coefficient: 3.02
Solvent content (%): 59.28
Release date: 2024-06-05
C-abl Kinase domain with the activator(cmpd29), N-(1-(3,4-dichlorophenyl)-4,5-dihydro-1H-pyrazol-3-yl)acetamide (PDB entry 6NPU)
Macromolecule: Tyrosine-protein kinase ABL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 298 residues
Sequence: MHHHHHHENLYFQGSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKELGK
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.1934
R free: 0.2342
Average B factor: 34.84
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 1 - 3 % PEG 400
2M AmSO4
0.1 HEPES pH 7.5
cryo: 20% Glycerol
Matthews coefficient: 2.99
Solvent content (%): 58.84
Ligand: 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE (STI)
Ligand formula: C29 H31 N7 O
Ligand molecular weight: 493.603
Ligand SMILES: Cc1ccc(cc1Nc2nccc(n2)c3cccnc3)NC(=O)c4ccc(cc4)CN5CCN(CC5)C
Ligand InChI: InChI=1S/C29H31N7O/c1-21-5-10-25(18-27(21)34-29-31-13-11-26(33-29)24-4-3-12-30-19-24)32-28(37)23-8-6-22(7-9-23)20-36-16-14-35(2)15-17-36/h3-13,18-19H,14-17,20H2,1-2H3,(H,32,37)(H,31,33,34)
Release date: 2019-03-13
Rapid development of two Factor IXa inhibitors from Hit to Lead (PDB entry 4Z0K)
Macromolecule: Coagulation factor IX
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.22
Sequence length: 62 residues
Sequence: MDVTCNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGRVSVSQTSKLTR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.147
R free: 0.165
Average B factor: 25.66
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 295
Crystal growth procedure: 50 mM Tris, pH 7.2,  1.2 M ammonium sulfate, 2.0 M sodium chloride
Matthews coefficient: 2.78
Solvent content (%): 55.7
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2015-05-20
Human carbonic anhydrase I in complex with Methyl 2-(benzenesulfonyl)-4-chloro-5-sulfamoylbenzoate (PDB entry 7Q0D)
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): 1.24
R work: 0.1309
R free: 0.1577
Average B factor: 17.893
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1 M Tris-HCl (pH 8.5), 0.2 M ammonium acetate and 24% PEG4000
Matthews coefficient: 2.37
Solvent content (%): 48.03
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: 2022-01-12
Crystal Structure of human phosphodiesterase 10 in complex with 6-methyl-N-(4-methylphenyl)pyrimidin-4-amine (PDB entry 5SIT)
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): 1.99
R work: 0.1961
R free: 0.2263
Average B factor: 38.303
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: 2.62
Solvent content (%): 53
Ligand: 6-methyl-N-(4-methylphenyl)pyrimidin-4-amine (JSY)
Ligand formula: C12 H13 N3
Ligand molecular weight: 199.252
Ligand SMILES: Cc1ccc(cc1)Nc2cc(ncn2)C
Ligand InChI: InChI=1S/C12H13N3/c1-9-3-5-11(6-4-9)15-12-7-10(2)13-8-14-12/h3-8H,1-2H3,(H,13,14,15)
Release date: 2022-10-12
Crystal structure of the DNA-binding domain of human myelin-gene regulatory factor (PDB entry 5ZHU)
Macromolecule: Myelin regulatory factor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4
Sequence length: 183 residues
Sequence: QSIKWQPHQQNKWATLYDANYKELPMLTYRVDADKGFNFSVGDDAFVCQKKNHFQVTVYIGMLGEPKYVKTPEGLKPLDCFYLKLHGVKLEALNQSINIEQSQSDRSKRPFNPVTVNLPPEQVTKVTVGRLHFSETTANNMRKKGKPNPDQRYFMLVVALQAHAQNQNYTLAAQISERIIVRA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.202
R work: 0.2281
R free: 0.2544
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.2M (NH4)2SO4, 0.1M HEPES pH7.0, 22.5% PEG 3350
Matthews coefficient: 2.56
Solvent content (%): 51.87
Release date: 2018-05-23
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z1262327505 (PDB entry 5RX3)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1726
R free: 0.1987
Average B factor: 21.195
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.09
Solvent content (%): 41.18
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: 2020-11-11
Aurora-A kinase domain in complex with vNAR-D01 S93R (PDB entry 5L8J)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 285 residues
Sequence: GAMESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPSNAQNKESASKQS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.68
R work: 0.1993
R free: 0.231
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M citric acid pH 5.0, 20% PEG 6000
Matthews coefficient: 2.3
Solvent content (%): 46.59
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2016-07-20
Complement factor D in complex with the inhibitor N-(3'-(aminomethyl)-[1,1'-biphenyl]-3-yl)-3-methylbutanamide (PDB entry 6FUJ)
Macromolecule: Complement factor D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.46
Sequence length: 232 residues
Sequence: ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLASAAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.21761
R free: 0.24388
Average B factor: 45.821
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 22-25% PEG3350, 100 mM HEPES pH 7.5, 2 mM inhibitor
Matthews coefficient: 2.97
Solvent content (%): 58.57
Ligand: ~{N}-[3-[3-(aminomethyl)phenyl]phenyl]-3-methyl-butanamide (E8B)
Ligand formula: C18 H22 N2 O
Ligand molecular weight: 282.38
Ligand SMILES: CC(C)CC(=O)Nc1cccc(c1)c2cccc(c2)CN
Ligand InChI: InChI=1S/C18H22N2O/c1-13(2)9-18(21)20-17-8-4-7-16(11-17)15-6-3-5-14(10-15)12-19/h3-8,10-11,13H,9,12,19H2,1-2H3,(H,20,21)
Release date: 2018-06-06
Crystal structure of SPRY domain of TRIM9 (PDB entry 7B2S)
Macromolecule: E3 ubiquitin-protein ligase TRIM9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 178 residues
Sequence: SMVAWFAFDPGSAHSDIILSNDNLTVTCSSYDDRVVLGKTGFSKGIHYWELTVDRYDNHPDPAFGVARMDVMKDVMLGKDDKAWAMYVDNNRSWFMHNNSHTNRTEGGITKGATIGVLLDFNRKNLTFFINDEQQGPIAFDNVEGLFFPAVSLNRNVQVTLHTGLPVPDFYSSRASIA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1416
R free: 0.1738
Average B factor: 14.448
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 30% PEG 8000, 0.2 M Ammonium sulfate
Matthews coefficient: 1.93
Solvent content (%): 36.21
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: 2021-01-13
Structure of C1156Y,L1198F Mutant Human Anaplastic Lymphoma Kinase in Complex with Crizotinib (PDB entry 5AAB)
Macromolecule: ALK TYROSINE KINASE RECEPTOR
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 327 residues
Sequence: MAHHHHHHNPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVYSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLEFMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIEYGPLVEEEEKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.21
R free: 0.246
Average B factor: 38.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 286
Crystal growth procedure: HANGING DROP VAPOR DIFFUSION AT 13 DEGREES C. 2 MICROLITERS OF PURIFIED PROTEIN SOLUTION (11-15 MG/ML) CONTAINING INHIBITOR COMPOUND AT A 2X STOICHIOMETRY OF INHIBITOR TO PROTEIN WERE COMBINED WITH 2 MICROLITERS OF SOLUTIONS CONTAINING: 0.2 M LITHIUM SULFATE, 17-21% PEG3350 AND 0.1M TRIS PH 7.6-8.5.
Matthews coefficient: 2.1
Solvent content (%): 41
Ligand: 3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine (VGH)
Ligand formula: C21 H22 Cl2 F N5 O
Ligand molecular weight: 450.337
Ligand SMILES: CC(c1c(ccc(c1Cl)F)Cl)Oc2cc(cnc2N)c3cnn(c3)C4CCNCC4
Ligand InChI: InChI=1S/C21H22Cl2FN5O/c1-12(19-16(22)2-3-17(24)20(19)23)30-18-8-13(9-27-21(18)25)14-10-28-29(11-14)15-4-6-26-7-5-15/h2-3,8-12,15,26H,4-7H2,1H3,(H2,25,27)/t12-/m1/s1
Release date: 2016-06-08
Lon protease proteolytic domain (PDB entry 6WYS)
Macromolecule: Lon protease homolog, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.53
Sequence length: 218 residues
Sequence: MGSDKIHHHHHHERMYDVTPPGVVMGLAWTAMGGSTLFVETSLRRPQDKDAKGDKDGSLEVTGQLGEVMKESARIAYTFARAFLMQHAPANDYLVTSHIHLHVPEGATPKDGPSAGCTIVTALLSLAMGRPVRQNLAMTGEVSLTGKILPVGGIKEKTIAAKRAGVTCIVLPAENKKDFYDLAAFITEGLEVHFVEHYREIFDIAFPDEQAEALAVER
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.229
R work: 0.188
R free: 0.2133
Average B factor: 57.4982
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M sodium chloride, 1.6M ammonium sulfate, 0.1M HEPES pH 7.5
Matthews coefficient: 3.77
Solvent content (%): 67.34
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: 2021-04-14
Human CYP3A4 bound to an inhibitor (PDB entry 6DA5)
Macromolecule: Cytochrome P450 3A4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14
Sequence length: 487 residues
Sequence: MAYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDGTVSGAHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.2164
R free: 0.2939
Crystallization method: MICROBATCH
Crystallization temperature (K): 293
Crystal growth procedure: peg 3350, sodium malonate
Matthews coefficient: 2.19
Solvent content (%): 43.74
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2019-04-03
Structure-Based Design of ASK1 Inhibitors as Potential First-in-Class Agents for Heart Failure (PDB entry 5UP3)
Macromolecule: Mitogen-activated protein kinase kinase kinase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 271 residues
Sequence: LLEYDYEYDENGDRVVLGKGTYGIVYAGRDLSNQVRIAIKEIPERDSRYSQPLHEEIALHKHLKHKNIVQYLGSFSENGFIKIFMEQVPGGSLSALLRSKWGPLKDNEQTIGFYTKQILEGLKYLHDNQIVHRDIKGDNVLINTYSGVLKISDFGTSKRLAGINPCTETFTGTLQYMAPEIIDKGPRGYGKAADIWSLGCTIIEMATGKPPFYELGEPQAAMFKVGMFKVHPEIPESMSAEAKAFILKCFEPDPDKRACANDLLVDEFLKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.2417
R free: 0.2888
Average B factor: 79.935
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 7% polyethylene glycol 2000 MME , 0.05M Ammonium Sulphate, 0.05M MES, pH 6.0
Matthews coefficient: 3.17
Solvent content (%): 61.17
Ligand: 2-{6-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]pyridin-2-yl}-2,3-dihydro-1H-isoindol-1-one (8GS)
Ligand formula: C18 H17 N5 O
Ligand molecular weight: 319.36
Ligand SMILES: CC(C)n1cnnc1c2cccc(n2)N3Cc4ccccc4C3=O
Ligand InChI: InChI=1S/C18H17N5O/c1-12(2)23-11-19-21-17(23)15-8-5-9-16(20-15)22-10-13-6-3-4-7-14(13)18(22)24/h3-9,11-12H,10H2,1-2H3
Release date: 2017-06-07
Crystal structure of PROTAC 1 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB (PDB entry 6HAY)
Macromolecule: Probable global transcription activator SNF2L2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4
Sequence length: 123 residues
Sequence: SMAEKLSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQKIAKEEE
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.192
R free: 0.223
Average B factor: 55.66
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.75
Crystallization temperature (K): 277
Crystal growth procedure: 18% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M HEPES, pH 7.75
Matthews coefficient: 2.61
Solvent content (%): 52.79
Ligand: (2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]ethoxy]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide (FX8)
Ligand formula: C46 H60 F N9 O8 S
Ligand molecular weight: 918.088
Ligand SMILES: Cc1c(scn1)c2ccc(c(c2)OCCOCCOCCN3CCN(CC3)c4cc(nnc4N)c5ccccc5O)CNC(=O)C6CC(CN6C(=O)C(C(C)(C)C)NC(=O)C7(CC7)F)O
Ligand InChI: InChI=1S/C46H60FN9O8S/c1-29-39(65-28-50-29)30-9-10-31(26-49-42(59)36-24-32(57)27-56(36)43(60)40(45(2,3)4)51-44(61)46(47)11-12-46)38(23-30)64-22-21-63-20-19-62-18-17-54-13-15-55(16-14-54)35-25-34(52-53-41(35)48)33-7-5-6-8-37(33)58/h5-10,23,25,28,32,36,40,57-58H,11-22,24,26-27H2,1-4H3,(H2,48,53)(H,49,59)(H,51,61)/t32-,36+,40-/m1/s1
Release date: 2019-06-12
Crystal structure of human NRMT2 in complex with alpha-N-monomethylated human CENP-A peptide (PDB entry 6KDS)
Macromolecule: Alpha N-terminal protein methyltransferase 1B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.299
Sequence length: 244 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMVINGEMQFYARAKLFYQEVPATEEGMMGNFIELSSPDIQASQKFLRKFVGGPGRAGTDCALDCGSGIGRVSKHVLLPVFNSVELVDMMESFLLEAQNYLQVKGDKVESYHCYSLQEFTPPFRRYDVIWIQWVSGHLTDKDLLAFLSRCRDGLKENGIIILKDNVAREGCILDLSDSSVTRDMDILRSLIRKSGLVVLGQEKQDGFPEQCIPVWMFALHSDRHS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.844
R work: 0.1783
R free: 0.2047
Average B factor: 31.1282
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.1
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M Tris pH 8.1, 14% w/v Polyethylene glycol 8000
Matthews coefficient: 2.32
Solvent content (%): 47.08
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: 2020-07-08
Cytochrome P450 3A4 bound to imidazole and an inhibitor (PDB entry 4D6Z)
Macromolecule: CYTOCHROME P450 3A4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.13.157
Sequence length: 487 residues
Sequence: MAYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSAETASHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDGTVSGAHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.18
R free: 0.2271
Crystallization pH: 7
Crystal growth procedure: CONDITION A3 FROM THE MORPHEUS CRYSTALLIZATION KIT (MOLECULAR DIMENSIONS), pH 7
Matthews coefficient: 2.55
Solvent content (%): 51.8
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2015-09-23
APOBEC3F Catalytic Domain Crystal Structure (PDB entry 5HX5)
Macromolecule: DNA dC->dU-editing enzyme APOBEC-3F
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4
Sequence length: 199 residues
Sequence: GPLGSPGIPGKEILRNPMEAMDPHIFYFHFKNLRKAYGRNESWLCFTMEVVKHHSPVSWKRGVFRNQVDPETGRHAERCFLSWFADDILSPNTNYEVTWYTSWSPCPECAGEVAEFLARHSNVNLTIKTARLYYFDDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPWDGLDYNFLDLDSKLQEILE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.2268
R free: 0.2644
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: PEG3350, MgCl2
Matthews coefficient: 1.97
Solvent content (%): 37.57
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: 2016-05-18