satarupa22/MacromolecularLigandDB huggingface dataset:
Fragment-based discovery of potent and selective DDR1/2 inhibitors (PDB entry 5BVN)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 324 residues
Sequence: GAMGSAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDGQAAQGPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.2523
R free: 0.3275
Average B factor: 29.02
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 10.0%w/v PEG 3350, 0.1M KNO3
Matthews coefficient: 2.45
Solvent content (%): 49.78
Ligand: IODIDE ION (IOD)
Ligand formula: I
Ligand molecular weight: 126.904
Ligand SMILES: [I-]
Ligand InChI: InChI=1S/HI/h1H/p-1
Release date: 2015-08-12
JAK2 JH2 in complex with JAK168 (PDB entry 6OBL)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.061
R work: 0.1975
R free: 0.239
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1M TRIS, PH 8.0 0.2M SODIUM ACETATE, 0.001 M TCEP, 12-24% PEG 4,000
Matthews coefficient: 2.17
Solvent content (%): 43.33
Ligand: [4-({5-amino-3-[(4-cyanophenyl)amino]-1H-1,2,4-triazole-1-carbonyl}amino)phenoxy]acetic acid (M4P)
Ligand formula: C18 H15 N7 O4
Ligand molecular weight: 393.356
Ligand SMILES: c1cc(ccc1C#N)Nc2nc(n(n2)C(=O)Nc3ccc(cc3)OCC(=O)O)N
Ligand InChI: InChI=1S/C18H15N7O4/c19-9-11-1-3-12(4-2-11)21-17-23-16(20)25(24-17)18(28)22-13-5-7-14(8-6-13)29-10-15(26)27/h1-8H,10H2,(H,22,28)(H,26,27)(H3,20,21,23,24)
Release date: 2020-03-25
Phospho-ERK2 bound to bivalent inhibitor SBP3 (PDB entry 5V62)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 351 residues
Sequence: GPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1709
R free: 0.2033
Average B factor: 41.355
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris-Bicine pH 8.5, 0.02 M each of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol, 1,3-Propanediol, 20% v/v PEG550MME, 10% w/v PEG20,000
Matthews coefficient: 2.92
Solvent content (%): 57.88
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: 2017-07-26
Structure of CHK1 10-pt. mutant complex with LRRK2 inhibitor 15 (PDB entry 7SUH)
Macromolecule: Serine/threonine-protein kinase Chk1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICILKMLNHENVIKFYGHRREGNIQYLFMELASGGSLFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPHNLLLDERDNLKIADYSLATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRPRVTSGGVSESPSGHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.46
R work: 0.176
R free: 0.242
Average B factor: 58.26
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7% PEG 8000, 0.1 M MES buffer PH 6.5, 20% ethylene glycol
Matthews coefficient: 2.31
Solvent content (%): 46.68
Ligand: 1-[5-chloro-4-({6-chloro-7-[1-(oxetan-3-yl)piperidin-4-yl]quinazolin-2-yl}amino)-1H-pyrazol-1-yl]-2-methylpropan-2-ol (BXI)
Ligand formula: C23 H28 Cl2 N6 O2
Ligand molecular weight: 491.413
Ligand SMILES: CC(C)(Cn1c(c(cn1)Nc2ncc3cc(c(cc3n2)C4CCN(CC4)C5COC5)Cl)Cl)O
Ligand InChI: InChI=1S/C23H28Cl2N6O2/c1-23(2,32)13-31-21(25)20(10-27-31)29-22-26-9-15-7-18(24)17(8-19(15)28-22)14-3-5-30(6-4-14)16-11-33-12-16/h7-10,14,16,32H,3-6,11-13H2,1-2H3,(H,26,28,29)
Release date: 2022-01-12
Crystal structure of TRIM7 bound to RACO-1 (PDB entry 7Y3C)
Macromolecule: E3 ubiquitin-protein ligase TRIM7,E3 ubiquitin-protein ligase TRIM7,TRIM7-RACO-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 194 residues
Sequence: KEEKVELTLDPDTANPRLILSLDLKGVRLGERAQDLPNHPCRFDTNTRVLASCGFSSGRHHWEVEVGSKDGWAFGVARESVRRKGLTPFTPEEGVWALQLNGGQYWAVTSPERSPLSCGHLSRVRVALDLEVGAVSFYAVEDMRHLYTFRVNFQERVFPLFSVCSTGTYLRIWPGGSGGSGGSSVGATLSMLLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.1627
R free: 0.1976
Average B factor: 25.9
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M Potassium sodium tartrate tetrahydrate, 26% w/v Polyethylene glycol 3,350
Matthews coefficient: 2.29
Solvent content (%): 46.22
Release date: 2022-08-03
IgCam3 of human MLCK1 (PDB entry 6C6M)
Macromolecule: Myosin light chain kinase, smooth muscle
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.18
Sequence length: 103 residues
Sequence: MEGQRDSAFPKFESKPQSQEVKENQTVKFRCEVSGIPKPEVAWFLEGTPVRRQEGSIEVYEDAGSHYLCLLKARTRDSGTYSCTASNAQGQLSCSWTLQVERL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.226
R free: 0.272
Average B factor: 81.4
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 200mM ammonium dihydrogen phosphate, 20% PEG3350
Matthews coefficient: 3.22
Solvent content (%): 61.78
Release date: 2019-01-23
Human Aurora A catalytic domain bound to FK932 (PDB entry 4ZTQ)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 285 residues
Sequence: GAMESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPSNCQNKESASKQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.20131
R free: 0.24624
Average B factor: 78.903
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 0.3 M Ammonium citrate dibasic, 
25% PEG 3350
Matthews coefficient: 2.58
Solvent content (%): 52.41
Ligand: (2Z,5Z)-2-[(4-ethylphenyl)imino]-3-(2-methoxyethyl)-5-(pyridin-4-ylmethylidene)-1,3-thiazolidin-4-one (4RM)
Ligand formula: C20 H21 N3 O2 S
Ligand molecular weight: 367.465
Ligand SMILES: CCc1ccc(cc1)N=C2N(C(=O)C(=Cc3ccncc3)S2)CCOC
Ligand InChI: InChI=1S/C20H21N3O2S/c1-3-15-4-6-17(7-5-15)22-20-23(12-13-25-2)19(24)18(26-20)14-16-8-10-21-11-9-16/h4-11,14H,3,12-13H2,1-2H3/b18-14-,22-20-
Release date: 2016-07-20
Crystal structure of the human platelet-activating factor receptor in complex with ABT-491 (PDB entry 5ZKQ)
Macromolecule: Platelet-activating factor receptor,Endolysin,Endolysin,Platelet-activating factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 438 residues
Sequence: GAPEPHDSSHMDSEFRYTLFPIVYSIIFVLGVIANGYVLWVFARLYPCKKFNEIKIFMVNLTMADMLFLITLPLWIVYYQNQGNWILPKFLCNVAGCLFFINTYCSVAFLGVITYNRYQAVTRPIKTAQANTRKRGISLSLVIWVAIVGAASYFLILDSTNTVPDSAGSGDVTRCFEHYEKGSVPVLIIHIFIVFSFFLVFLIILFCNLVIIRTLLMQPVNIFEMLRIDEGGGSGGDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYAEVKRRDLWMACTVLAVFIICFVPHHVVQLPWTLAELGFQDSKFHQAINDAHQVTLCLLSTNCVLNPVIYCFLTKKFRKHLTEKFYSMRSSRKEFLEVLFQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.203
R free: 0.235
Average B factor: 85.97
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293
Crystal growth procedure: HEPES, PEG 400, MgSO4
Matthews coefficient: 3.54
Solvent content (%): 65.23
Ligand: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (OLC)
Ligand formula: C21 H40 O4
Ligand molecular weight: 356.54
Ligand SMILES: CCCCCCCCC=CCCCCCCCC(=O)OCC(CO)O
Ligand InChI: InChI=1S/C21H40O4/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-21(24)25-19-20(23)18-22/h9-10,20,22-23H,2-8,11-19H2,1H3/b10-9-/t20-/m1/s1
Release date: 2018-06-20
Crystal structure of allosteric inhibitor, ARQ 092, in complex with autoinhibited form of AKT1 (PDB entry 5KCV)
Macromolecule: RAC-alpha serine/threonine-protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 460 residues
Sequence: MGHHHHHHENLYFQGSDVAIVKEGWLHKRGEYIKTWRPRYFLLKNDGTFIGYKERPQDVDQREAPLNNFSVAQCQLMKTERPRPNTFIIRCLQWTTVIERTFHVETPEEREEWTTAIQTVADGLKKQAAAEMDFRSGSPSDNSGAEEMEVSLAKPKHRVTMNEFEYLKLLGKGTFGKVILVKEKATGRYYAMKILKKEVIVAKDEVAHTLTENRVLQNSRHPFLTALKYSFQTHDRLCFVMEYANGGELFFHLSRERVFSEDRARFYGAEIVSALDYLHSEKNVVYRDLKLENLMLDKDGHIKITDFGLCKEGIKDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILMEEIRFPRTLGPEAKSLLSGLLKKDPKQRLGGGSEDAKEIMQHRFFAGIVWQHVYEKKLSPPFKPQVTSETDTRYFDEEFTAQM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.20961
R free: 0.2686
Average B factor: 67.735
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 16% butanol, 10mM ammonium sulfate, 0.1% 2-mercaptoethanol, 15% ethylene glycol, 50mM Tris, pH 7.5
Matthews coefficient: 2.36
Solvent content (%): 47.78
Ligand: 3-[3-[4-(1-azanylcyclobutyl)phenyl]-5-phenyl-imidazo[4,5-b]pyridin-2-yl]pyridin-2-amine (6S1)
Ligand formula: C27 H24 N6
Ligand molecular weight: 432.52
Ligand SMILES: c1ccc(cc1)c2ccc3c(n2)n(c(n3)c4cccnc4N)c5ccc(cc5)C6(CCC6)N
Ligand InChI: InChI=1S/C27H24N6/c28-24-21(8-4-17-30-24)25-32-23-14-13-22(18-6-2-1-3-7-18)31-26(23)33(25)20-11-9-19(10-12-20)27(29)15-5-16-27/h1-4,6-14,17H,5,15-16,29H2,(H2,28,30)
Release date: 2016-06-29
ERK2 covelently bound to RU68 cyclohexenone based inhibitor (PDB entry 8PSY)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 364 residues
Sequence: GSASMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.1897
R free: 0.2318
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG1000, 0.1M Na-citrate pH 5.5
Matthews coefficient: 2.55
Solvent content (%): 51.7
Ligand: AMP PHOSPHORAMIDATE (AN2)
Ligand formula: C10 H16 N6 O9 P2
Ligand molecular weight: 426.216
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(N)O)O)O)N
Ligand InChI: InChI=1S/C10H16N6O9P2/c11-8-5-9(14-2-13-8)16(3-15-5)10-7(18)6(17)4(24-10)1-23-27(21,22)25-26(12,19)20/h2-4,6-7,10,17-18H,1H2,(H,21,22)(H2,11,13,14)(H3,12,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2024-07-24
Structure of hemiacetylated human butyrylcholinesterase upon reaction with 8-(3-(4-(prop-2-yn-1-yl)piperazin-1-yl)propoxy)quinoline-2-carbaldehyde (PDB entry 7ZPB)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 529 residues
Sequence: EDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.31
R work: 0.1771
R free: 0.2172
Average B factor: 58.16
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate
Matthews coefficient: 3.19
Solvent content (%): 61.44
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2023-02-01
Crystal structure of CK2alpha with 3-(3-chloro-4-(phenyl)benzylamino)propan-1-ol bound (PDB entry 5CT0)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.008
R work: 0.1998
R free: 0.2202
Average B factor: 51.48
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 107mM Mes pH 6.5, 29% glycerol ethoxylate, 1 M ammonium acetate
Matthews coefficient: 2.2
Solvent content (%): 44.18
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: 2016-11-30
Human GRK2 in complex with Gbetagamma subunits and CCG258747 (PDB entry 6U7C)
Macromolecule: Beta-adrenergic receptor kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.15
Sequence length: 689 residues
Sequence: MADLEAVLADVSYLMAMEKSKATPAARASKKILLPEPSIRSVMQKYLEDRGEVTFEKIFSQKLGYLLFRDFCLNHLEEARPLVEFYEEIKKYEKLETEEERVARSREIFDSYIMKELLACSHPFSKSATEHVQGHLGKKQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFCQWKNVELNIHLTMNDFSVHRIIGRGGFGEVYGCRKADTGKMYAMKCLDKKRIKMKQGETLALNERIMLSLVSTGDCPFIVCMSYAFHTPDKLSFILDLMNGGDLHYHLSQHGVFSEADMRFYAAEIILGLEHMHNRFVVYRDLKPANILLDEHGHVRISDLGLACDFSKKKPHASVGTHGYMAPEVLQKGVAYDSSADWFSLGCMLFKLLRGHSPFRQHKTKDKHEIDRMTLTMAVELPDSFSPELRSLLEGLLQRDVNRRLGCLGRGAQEVKESPFFRSLDWQMVFLQKYPPPLIPPRGEVNAADAFDIGSFDEEDTKGIKLLDSDQELYRNFPLTISERWQQEVAETVFDTINAETDRLEARKKAKNKQLGHEEDYALGKDCIMHGYMSKMGNPFLTQWQRRYFYLFPNRLEWRGEGEAPQSLLTMEEIQSVEETQIKERKCLLLKIRGGKQFILQCDSDPELVQWKKELRDAYREAQQLVQRVPKMKNKPRSPVVELSKVPLVQRGSANGL
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.44
R work: 0.2366
R free: 0.2624
Average B factor: 52.51
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 50 mM MES pH 6.0, 1.1 M NaCl, 6% PEG 3350
Matthews coefficient: 3.13
Solvent content (%): 60.72
Ligand: 5-[(3S,4R)-3-{[(2H-1,3-benzodioxol-5-yl)oxy]methyl}piperidin-4-yl]-2-fluoro-N-[(2H-indazol-3-yl)methyl]benzamide (Q1Y)
Ligand formula: C28 H27 F N4 O4
Ligand molecular weight: 502.537
Ligand SMILES: c1ccc2c(c1)c([nH]n2)CNC(=O)c3cc(ccc3F)C4CCNCC4COc5ccc6c(c5)OCO6
Ligand InChI: InChI=1S/C28H27FN4O4/c29-23-7-5-17(11-22(23)28(34)31-14-25-21-3-1-2-4-24(21)32-33-25)20-9-10-30-13-18(20)15-35-19-6-8-26-27(12-19)37-16-36-26/h1-8,11-12,18,20,30H,9-10,13-16H2,(H,31,34)(H,32,33)/t18-,20-/m0/s1
Release date: 2020-04-15
Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB (PDB entry 7Z76)
Macromolecule: von Hippel-Lindau disease tumor suppressor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 162 residues
Sequence: GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.32
R work: 0.178
R free: 0.202
Average B factor: 27.12
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 293
Crystal growth procedure: 14.5 % PEG 3350, 0.1 M BIS-TRIS propane pH 5.8, 100 mM sodium iodide
Matthews coefficient: 2.87
Solvent content (%): 57.17
Ligand: IODIDE ION (IOD)
Ligand formula: I
Ligand molecular weight: 126.904
Ligand SMILES: [I-]
Ligand InChI: InChI=1S/HI/h1H/p-1
Release date: 2022-09-14
Crystal structure of the PI3KC2alpha PX domain in space group P432 (PDB entry 6BUB)
Macromolecule: Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.154
Sequence length: 143 residues
Sequence: SNADEPILSFSPKTYSFRQDGRIKEVSVFTYHKKYNPDKHYIYVVRILREGQIEPSFVFRTFDEFQELHNKLSIIFPLWKLPGFPNRMVLGRTHIKDVAAKRKIELNSYLQSLMNASTDVAECDLVCTFFHPLLRDEKAEGIA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.604
R work: 0.2377
R free: 0.2734
Average B factor: 47.7949
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: (NH4)2SO4
Matthews coefficient: 3.92
Solvent content (%): 68.6
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: 2018-10-17
WWP1 close conformation (PDB entry 6J1X)
Macromolecule: NEDD4-like E3 ubiquitin-protein ligase WWP1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 550 residues
Sequence: GPGSEFRPQPLPPGWERRVDDRRRVYYVDHNTRTTTWQRPTMESVRNFEQWQSQRNQLQGAMQQFNQRYLYSASMLAAENDPYGPLPPGWEKRVDSTDRVYFVNHNTKTTQWEDPRTQGLQNEEPLPEGWEIRYTREGVRYFVDHNTRTTTFKDPRNGKSSVTKGGPQIAYERGFRWKLAHFRYLCQSNALPSHVKINVSRQTLFEDSFQQIMALKPYDLRRRLYVIFRGEEGLDYGGLAREWFFLLSHEVLNPMYCLFEYAGKNNYCLQINPASTINPDHLSYFCFIGRFIAMALFHGKFIDTGFSLPFYKRMLSKKLTIKDLESIDTEFYNSLIWIRDNNIEECGLEMYFSVDMEILGKVTSHDLKLGGSNILVTEENKDEYIGLMTEWRFSRGVQEQTKAFLDGFNEVVPLQWLQYFDEKELEVMLCGMQEVDLADWQRNTVYRHYTRNSKQIIWFWQFVKETDNEVRMRLLQFVTGTCRLPLGGFAELMGSNGPQKFCIEKVGKDTWLPRSHTCFNRLDLPPYKSYEQLKEKLLFAIEETEGFGQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2195
R free: 0.2705
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289.15
Crystal growth procedure: 100mM Tris-HCl pH 7.0, 15% v/v reagent alcohol
Matthews coefficient: 2.31
Solvent content (%): 46.68
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: 2019-07-24
Structure of DYRK1A in complex with compound 38 (PDB entry 7AJV)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 359 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1805
R free: 0.2193
Average B factor: 32.945
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 12% PEG3350, 0.2M ammonium sulphate, 0.05M Mg sulphate, 0.05M Na citrate buffer pH 5.6
Matthews coefficient: 2.39
Solvent content (%): 48.45
Ligand: 4-(2,3-dibutylimidazo[4,5-b]pyridin-5-yl)pyridine-2,6-diamine (RKK)
Ligand formula: C19 H26 N6
Ligand molecular weight: 338.45
Ligand SMILES: CCCCc1nc2ccc(nc2n1CCCC)c3cc(nc(c3)N)N
Ligand InChI: InChI=1S/C19H26N6/c1-3-5-7-18-22-15-9-8-14(13-11-16(20)24-17(21)12-13)23-19(15)25(18)10-6-4-2/h8-9,11-12H,3-7,10H2,1-2H3,(H4,20,21,24)
Release date: 2021-05-26
Crystal structure of hMTH1 F27A in complex with TH scaffold 1 in the absence of acetate (PDB entry 6GLJ)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 182 residues
Sequence: MKHHHHHHPMSDYDIPTTENLYFQGAMGASRLYTLVLVLQPQRVLLGMKKRGAGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.301
R work: 0.1774
R free: 0.1983
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: crystallized in: 23-27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5

soaked in: 0.27 M ammonium sulfate, 17% glycerol, 27% PEG4000, 50 mM compound
Matthews coefficient: 1.71
Solvent content (%): 28.11
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: 2019-02-20