satarupa22/MacromolecularLigandDB huggingface dataset:
The complex between TIL 1383i TCR and human Class I MHC HLA-A2 with the bound Tyrosinase(369-377)(N371D) nonameric peptide (PDB entry 7RK7)
Macromolecule: HLA class I histocompatibility antigen, A alpha chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 275 residues
Sequence: GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE
Oligomeric state: Hetero 5-mer
Stoichiometry: A1, B1, C1, D1, E1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.54
R work: 0.2111
R free: 0.2549
Average B factor: 89.53
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 16% PEG 3350, 2% tacsimate, 100mM Tris (pH 8.5)
Matthews coefficient: 2.88
Solvent content (%): 57.26
Release date: 2022-11-02
Crystal structure of DDT with the selective inhibitor 2,5-Pyridinedicarboxylic Acid (PDB entry 8DBB)
Macromolecule: D-dopachrome decarboxylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.1.1.84
Sequence length: 118 residues
Sequence: MPFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL
Oligomeric state: Homo 3-mer
Stoichiometry: A3
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.12119
R free: 0.15663
Average B factor: 9.603
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M sodium citrate, pH 5.20, 0.2 M ammonium acetate, 24-30% PEG4000
Matthews coefficient: 2.15
Solvent content (%): 42.89
Ligand: pyridine-2,5-dicarboxylic acid (R3K)
Ligand formula: C7 H5 N O4
Ligand molecular weight: 167.119
Ligand SMILES: c1cc(ncc1C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C7H5NO4/c9-6(10)4-1-2-5(7(11)12)8-3-4/h1-3H,(H,9,10)(H,11,12)
Release date: 2023-03-08
Crystal structure of human Pim-1 kinase in complex with a consensuspeptide and (R)-3-(2-((isoquinolin-5-ylmethyl)(methyl)carbamoyl)phenyl)pyrrolidin-1-ium (PDB entry 5N5M)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 313 residues
Sequence: MLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.1659
R free: 0.2052
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: HEPES
MgCl2
Glycerol
DTT
BIS-TRIS-propane
PEG3350
Ethylene-glycol
DMSO
Matthews coefficient: 3.16
Solvent content (%): 61
Ligand: ~{N}-(isoquinolin-5-ylmethyl)-~{N}-methyl-2-[(3~{R})-pyrrolidin-3-yl]benzamide (8O8)
Ligand formula: C22 H23 N3 O
Ligand molecular weight: 345.438
Ligand SMILES: CN(Cc1cccc2c1ccnc2)C(=O)c3ccccc3C4CCNC4
Ligand InChI: InChI=1S/C22H23N3O/c1-25(15-18-6-4-5-16-13-24-12-10-19(16)18)22(26)21-8-3-2-7-20(21)17-9-11-23-14-17/h2-8,10,12-13,17,23H,9,11,14-15H2,1H3/t17-/m0/s1
Release date: 2018-03-07
PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13854a (PDB entry 5R53)
Macromolecule: Uridine diphosphate glucose pyrophosphatase NUDT22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.45
Sequence length: 304 residues
Sequence: SMDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPKFRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADPLGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVHELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLSGGPEAHESTGIFFVETQNVRRLPETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALLPPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1845
R free: 0.2122
Average B factor: 20.993
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Matthews coefficient: 2.02
Solvent content (%): 39.25
Ligand: ~{N}-[(3~{R})-2-oxidanylideneazepan-3-yl]furan-2-carboxamide (RYG)
Ligand formula: C11 H14 N2 O3
Ligand molecular weight: 222.24
Ligand SMILES: c1cc(oc1)C(=O)NC2CCCCNC2=O
Ligand InChI: InChI=1S/C11H14N2O3/c14-10-8(4-1-2-6-12-10)13-11(15)9-5-3-7-16-9/h3,5,7-8H,1-2,4,6H2,(H,12,14)(H,13,15)/t8-/m1/s1
Release date: 2020-07-01
Crystal structure of human promyeloperoxidase (proMPO) (PDB entry 5MFA)
Macromolecule: Myeloperoxidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.2.2
Sequence length: 697 residues
Sequence: AAPAVLGEVDTSLVLSSMEEAKQLVDKAYKERRESIKQRLRSGSASPMELLSYFKQPVAATRTAVRAADYLHVALDLLERKLRSLWRRPFNVTDVLTPAQLNVLSKSSGCAYQDVGVTCPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPAARASFVTGVNCETSCVQQPPCFPLKIPPNDPRIKNQADCIPFFRSCPACPGSNITIRNQINALTSFVDASMVYGSEEPLARNLRNMSNQLGLLAVNQRFQDNGRALLPFDNLHDDPCLLTNRSARIPCFLAGDTRSSEMPELTSMHTLLLREHNRLATELKSLNPRWDGERLYQEARKIVGAMVQIITYRDYLPLVLGPTAMRKYLPTYRSYNDSVDPRIANVFTNAFRYGHTLIQPFMFRLDNRYQPMEPNPRVPLSRVFFASWRVVLEGGIDPILRGLMATPAKLNRQNQIAVDEIRERLFEQVMRIGLDLPALNMQRSRDHGLPGYNAWRRFCGLPQPETVGQLGTVLRNLKLARKLMEQYGTPNNIDIWMGGVSEPLKRKGRVGPLLACIIGTQFRKLRDGDRFWWENEGVFSMQQRQALAQISLPRIICDNTGITTVSKNNIFMSNSYPRDFVNCSTLPALNLASWREAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1233
R free: 0.1429
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295.15
Crystal growth procedure: 10% w/v PEG20000, 20% PEG MME 550, 0.1 mM Tris-Bicine, pH 8.5, 0.05 mM CaCl2
Matthews coefficient: 2.59
Solvent content (%): 52.51
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: 2017-04-05
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMSOA000281b (PDB entry 5QF6)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.765
R work: 0.192
R free: 0.2083
Average B factor: 41.4411
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.28
Solvent content (%): 62.55
Ligand: 6-methyl-2-oxo-4-(trifluoromethyl)-1,2-dihydropyridine-3-carbonitrile (JNY)
Ligand formula: C8 H5 F3 N2 O
Ligand molecular weight: 202.133
Ligand SMILES: CC1=CC(=C(C(=O)N1)C#N)C(F)(F)F
Ligand InChI: InChI=1S/C8H5F3N2O/c1-4-2-6(8(9,10)11)5(3-12)7(14)13-4/h2H,1H3,(H,13,14)
Release date: 2018-10-10
Crystal structure of apo EGFR kinase domain (PDB entry 7SI1)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1923
R free: 0.2146
Average B factor: 27.99
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M MES pH 7.0, 1M Na/K Tartrate
Matthews coefficient: 3.31
Solvent content (%): 62.9
Ligand: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID (MES)
Ligand formula: C6 H13 N O4 S
Ligand molecular weight: 195.237
Ligand SMILES: C1COCC[NH+]1CCS(=O)(=O)[O-]
Ligand InChI: InChI=1S/C6H13NO4S/c8-12(9,10)6-3-7-1-4-11-5-2-7/h1-6H2,(H,8,9,10)
Release date: 2022-10-26
Crystal Structure of KRAS4b-G13D (GMPPNP-bound) in complex with RAS-binding domain (RBD) of RAF1/CRAF (PDB entry 8EPW)
Macromolecule: RAF proto-oncogene serine/threonine-protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 80 residues
Sequence: SKTSNTIRVFLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQPECCAVFRLLHEHKGKKARLDWNTDAASLIGEELQVDFL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1916
R free: 0.2528
Average B factor: 38.0752
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.15 M potassium bromide, 30% PEG 2000 MME
Matthews coefficient: 1.86
Solvent content (%): 33.9
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2023-06-07
Human butyrylcholinesterase in complex with huprine 19 (PDB entry 6EQQ)
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): 2.40000447819
R work: 0.1707807062
R free: 0.195683987417
Average B factor: 60.3772836568
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES buffer, 2.1 M Ammonium sulfate
Matthews coefficient: 3.36
Solvent content (%): 63.42
Ligand: huprine 19 (H19)
Ligand formula: C18 H21 Cl N3
Ligand molecular weight: 314.832
Ligand SMILES: c1cc2c(cc1Cl)nc3c(c2N)C4CC(C3)CC(=C4)CC[NH3+]
Ligand InChI: InChI=1S/C18H20ClN3/c19-13-1-2-14-15(9-13)22-16-8-11-5-10(3-4-20)6-12(7-11)17(16)18(14)21/h1-2,6,9,11-12H,3-5,7-8,20H2,(H2,21,22)/p+1/t11-,12+/m1/s1
Release date: 2017-12-13
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 11 (PDB entry 8BM8)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.68
R work: 0.1897
R free: 0.2249
Average B factor: 25.45
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 37,5 % MPD_PEG1000_PEG3350, 100 mM Morpheus Amino Acids Mix, 100 mM Bis-Tris pH 6.0
Matthews coefficient: 1.92
Solvent content (%): 35.89
Ligand: ~{N}-(3-cyanophenyl)-4-methyl-3-[(1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]benzamide (QT1)
Ligand formula: C26 H20 N8 O
Ligand molecular weight: 460.49
Ligand SMILES: Cc1ccc(cc1Nc2c3cnn(c3nc(n2)c4cccnc4)C)C(=O)Nc5cccc(c5)C#N
Ligand InChI: InChI=1S/C26H20N8O/c1-16-8-9-18(26(35)30-20-7-3-5-17(11-20)13-27)12-22(16)31-24-21-15-29-34(2)25(21)33-23(32-24)19-6-4-10-28-14-19/h3-12,14-15H,1-2H3,(H,30,35)(H,31,32,33)
Release date: 2024-06-05
Identification of a New Zinc Binding Chemotype by Fragment Screening (PDB entry 5TY8)
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): 1.45
R work: 0.12106
R free: 0.16269
Average B factor: 14.582
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 281
Crystal growth procedure: the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3; concentrated CA II at ~10 mg mL-1 was set up with seeding; dry compound was added to crystals several days before harvesting and data collection
Matthews coefficient: 2.1
Solvent content (%): 41.44
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: 2017-08-30
AMP-Activated protein kinase (AMPK) inhibition by SBI-0206965: alpha 2 kinase domain bound to SBI-0206965 (PDB entry 6BX6)
Macromolecule: 5'-AMP-activated protein kinase catalytic subunit alpha-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 276 residues
Sequence: GPKHDGRVKIGHYVLGDTLGVGTFGKVKIGEHQLTGHKVAVKILNRQKIRSLDVVGKIKREIQNLKLFRHPHIIKLYQVISTPTDFFMVMEYVSGGELFDYICKHGRVEEMEARRLFQQILSAVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRDSCGSPNYAAPEVISGRLYAGPEVDIWSCGVILYALLCGTLPFDDEHVPTLFKKIRGGVFYIPEYLNRSVATLLMHMLQVDPLKRATIKDIREHEWFKQDLPSYLFPE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.252
R free: 0.28
Average B factor: 111.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 293
Crystal growth procedure: 9-14 % ethanol, 5 mM magnesium chloride, 3-7 mM manganese chloride, 10 mM TCEP and 0.1 M Tris, pH 9.5.
Matthews coefficient: 2.37
Solvent content (%): 48.15
Ligand: 2-({5-bromo-2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}oxy)-N-methylbenzene-1-carboximidic acid (EDJ)
Ligand formula: C21 H21 Br N4 O5
Ligand molecular weight: 489.319
Ligand SMILES: CNC(=O)c1ccccc1Oc2c(cnc(n2)Nc3cc(c(c(c3)OC)OC)OC)Br
Ligand InChI: InChI=1S/C21H21BrN4O5/c1-23-19(27)13-7-5-6-8-15(13)31-20-14(22)11-24-21(26-20)25-12-9-16(28-2)18(30-4)17(10-12)29-3/h5-11H,1-4H3,(H,23,27)(H,24,25,26)
Release date: 2018-05-09
Human carbonic anhydrase II in complex with 4-(2-aminoethylsulfanyl)-2,3,5,6-tetrafluoro-N-methyl-benzenesulfonamide (PDB entry 7AGN)
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): 1.15
R work: 0.1474
R free: 0.1861
Average B factor: 16.849
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M sodium bicine (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7)
Matthews coefficient: 2.06
Solvent content (%): 40.31
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: 2021-09-01
Crystal Structure of EGFR-T790M/V948R in Complex with TAK-788 (PDB entry 7A6K)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 333 residues
Sequence: GSHMASGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1919
R free: 0.2202
Average B factor: 51.6092
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25.0 % PEG3350, 100 mM MgSO4, 4 % ethylen glycole, 6.8 mg/mL EGFR-T790M/V948R (in 100 mM NaCl, 25 mM Tris-HCl, 10 % glycerol, 1 mM TCEP, pH 8.0) 1 ul reservoir + 1 ul protein solution)
Matthews coefficient: 1.76
Solvent content (%): 29.93
Ligand: propan-2-yl 2-[[4-[2-(dimethylamino)ethyl-methyl-amino]-2-methoxy-5-(propanoylamino)phenyl]amino]-4-(1-methylindol-3-yl)pyrimidine-5-carboxylate (R28)
Ligand formula: C32 H41 N7 O4
Ligand molecular weight: 587.712
Ligand SMILES: CCC(=O)Nc1cc(c(cc1N(C)CCN(C)C)OC)Nc2ncc(c(n2)c3cn(c4c3cccc4)C)C(=O)OC(C)C
Ligand InChI: InChI=1S/C32H41N7O4/c1-9-29(40)34-24-16-25(28(42-8)17-27(24)38(6)15-14-37(4)5)35-32-33-18-22(31(41)43-20(2)3)30(36-32)23-19-39(7)26-13-11-10-12-21(23)26/h10-13,16-20H,9,14-15H2,1-8H3,(H,34,40)(H,33,35,36)
Release date: 2022-02-23
EGFR kinase (T790M/L858R) with inhibitor compound 27: ~{N}-(1~{H}-indazol-3-yl)-7,7-dimethyl-2-(2-methylpyrazol-3-yl)-5~{H}-furo[3,4-d]pyrimidin-4-amine (PDB entry 5EDR)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1906
R free: 0.2151
Average B factor: 77.17
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: PEG 10K, ethylene glycol
Matthews coefficient: 3.66
Solvent content (%): 66.36
Ligand: ~{N}-(1~{H}-indazol-3-yl)-7,7-dimethyl-2-(2-methylpyrazol-3-yl)-5~{H}-furo[3,4-d]pyrimidin-4-amine (5N4)
Ligand formula: C19 H19 N7 O
Ligand molecular weight: 361.4
Ligand SMILES: CC1(c2c(c(nc(n2)c3ccnn3C)Nc4c5ccccc5[nH]n4)CO1)C
Ligand InChI: InChI=1S/C19H19N7O/c1-19(2)15-12(10-27-19)16(23-18(21-15)14-8-9-20-26(14)3)22-17-11-6-4-5-7-13(11)24-25-17/h4-9H,10H2,1-3H3,(H2,21,22,23,24,25)
Release date: 2015-12-02
Crystal structure of human carbonic anhydrase isozyme XIII with N-butyl-2,4-dichloro-5-sulfamoyl-benzamide (PDB entry 6G5U)
Macromolecule: Carbonic anhydrase 13
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 263 residues
Sequence: MMSRLSWGYREHNGPIHWKEFFPIADGDQQSPIEIKTKEVKYDSSLRPLSIKYDPSSAKIISNSGHSFNVDFDDTENKSVLRGGPLTGSYRLRQVHLHWGSADDHGSEHIVDGVSYAAELHVVHWNSDKYPSFVEAAHEPDGLAVLGVFLQIGEPNSQLQKITDTLDSIKEKGKQTRFTNFDLLSLLPPSWDYWTYPGSLTVPPLLESVTWIVLKQPINISSQQLAKFRSLLCTAEGEAAAFLVSNHRPPQPLKGRKVRASFH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1924
R free: 0.229
Average B factor: 16.5456
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M ammonium citrate (pH 5.0) and 18% PEG
4000
Matthews coefficient: 2.22
Solvent content (%): 44.2
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: 2019-03-13
GTPASE HRAS IN COMPLEX WITH ZN-CYCLEN AT 200 MPA PRESSURE (PDB entry 8OSM)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 166 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1712
R free: 0.2241
Average B factor: 35.79
Crystallization method: BATCH MODE
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 40 MM TRIS HCL, 10 MM MGCL2, 2 MM DTE,
26-30 % PEG-400
Matthews coefficient: 1.88
Solvent content (%): 34.7
Ligand: TRIETHYLENE GLYCOL (PGE)
Ligand formula: C6 H14 O4
Ligand molecular weight: 150.173
Ligand SMILES: C(COCCOCCO)O
Ligand InChI: InChI=1S/C6H14O4/c7-1-3-9-5-6-10-4-2-8/h7-8H,1-6H2
Release date: 2024-05-08
Thrombin in complex with 4-Methoxy-N-(2-pyridinyl)benzamide (PDB entry 5AF9)
Macromolecule: THROMBIN HEAVY CHAIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 258 residues
Sequence: IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.18
R work: 0.1214
R free: 0.1372
Average B factor: 20.6
Crystallization pH: 7.5
Crystal growth procedure: SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
Matthews coefficient: 2.46
Solvent content (%): 49.97
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2015-08-26