satarupa22/MacromolecularLigandDB huggingface dataset:
Design and Optimization of Biaryl Ether Aryl Sulfonamides as Selective Inhibitors of NaV1.7: Discovery of Clinical Candidate PF-05089771 (PDB entry 5K7K)
Macromolecule: Cytochrome P450 2C9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.13.80
Sequence length: 477 residues
Sequence: MAKKTSSGRGKLPPGPTPLPVIGNILQIGIKDISKSLTNLSKVYGPVFTLYFGLKPIVVLHGYEAVKEALIDLGEEFSGRGIFPLAERANRGFGIVFSNGKKWKEIRRFSLMTLRNFGMGKRSIEDRVQEEARCLVEELRKTKASPCDPTFILGCAPCNVICSIIFHKRFDYKDQQFLNLMEKLNENIKILSSPWIQICNNFSPIIDYFPGTHNKLLKNVAFMKSYILEKVKEHQESMDMNNPQDFIDCFLMKMEKEKHNQPSEFTIESLENTAVDLFGAGTETTSTTLRYALLLLLKHPEVTAKVQEEIERVIGRNRSPCMQDRSHMPYTDAVVHEVQRYIDLLPTSLPHAVTCDIKFRNYLIPKGTTILISLTSVLHDNKEFPNPEMFDPHHFLDEGGNFKKSKYFMPFSAGKRICVGEALAGMELFLFLTSILQNFNLKSLVDPKNLDTTPVVNGFASVPPFYQLCFIPIHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.22437
R free: 0.27194
Average B factor: 59.48
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100mM Hepes at 8.5  with 2% Peg 4K. crystallizer Alec Tucker
 Cryoprotectand 40% peg 4K
Matthews coefficient: 2.53
Solvent content (%): 51.38
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: 2017-06-07
Ankyrin domain of SKD3 (PDB entry 8DEH)
Macromolecule: Caseinolytic peptidase B protein homolog
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 223 residues
Sequence: AAASNKDAALLEAARANNMQEVSRLLSEGADVNAKHRLGWTALMVAAINRNNSVVQVLLAAGADPNLGDDFSSVYKTAKEQGIHSLEDGGQDGASRHITNQWTSALEFRRWLGLPAGVLITREDDFNNRLNNRASFKGCTALHYAVLADDYRTVKELLDGGANPLQRNEMGHTPLDYAREGEVMKLLRTSEAKYQEKQRKREAEERRRFPLEQRLKEHIIGQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.815
R work: 0.1633
R free: 0.1894
Average B factor: 25.9808
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 287
Crystal growth procedure: 50 mM EPPS pH 8.0, 35% (v/v) PEP426,
and 250 mM ammonium sulfate
Matthews coefficient: 2.4
Solvent content (%): 48.78
Release date: 2023-04-19
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with PCM-0102141-001 (PDB entry 7G9C)
Macromolecule: Rho guanine nucleotide exchange factor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 245 residues
Sequence: SMEMDEKDFAADSWSLAVDSSFLQQHKKEVMKQQDVIYELIQTELHHVRTLKIMTRLFRTGMLEELHLEPGVVQGLFPCVDELSDIHTRFLSQLLERRRQALCPGSTRNFVIHRLGDLLISQFSGPSAEQMCKTYSEFCSRHSKALKLYKELYARDKRFQQFIRKVTRPAVLKRHGVQECILLVTQRITKYPLLISRILQHSHGIEEERQDLTTALGLVKELLSNVDEGIYQLEKGARLQEIYNR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.686
R work: 0.1945
R free: 0.2742
Average B factor: 52.04
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.49
Solvent content (%): 50.62
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2023-07-12
Comparison of the structure and activity of glycosylated and aglycosylated Human Carboxylesterase 1 (PDB entry 5A7H)
Macromolecule: LIVER CARBOXYLESTERASE 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.1
Sequence length: 531 residues
Sequence: SPPVVDTVHGKVLGKFVSLEGFAQPVAIFLGIPFAKPPLGPLRFTPPQPAEPWSFVKQATSYPPMCTQDPKAGQLLSELFTNRKENIPLKLSEDCLYLNIYTPADLTKKNRLPVMVWIHGGGLMVGAASTYDGLALAAHENVVVVTIQYRLGIWGFFSTGDEHSRGNWGHLDQVAALRWVQDNIASFGGNPGSVTIFGESAGGESVSVLVLSPLAKNLFHRAISESGVALTSVLVKKGDVKPLAEQIAITAGCKTTTSAVMVHCLRQKTEEELLETTLKMKFLSLDLQGDPRESQPLLGTVIDGMLLLKTPEELQAERNFHTVPYMVGINKQEFGWLIPMLMSYPLSEGQLDQKTAMSLLWKSYPLVCIAKELIPEATEKYLGGTDDTVKKKDLFLDLIADVMFGVPSVIVARNHRDAGAPTYMYEFQYRPSFSSDMKPKTVIGDHGDELFSVFGAPFLKEGASEEEIRLSKMVMKFWANFARNGNPNGEGLPHWPEYNQKEGYLQIGANTQAAQKLKDKEVAFWTNLFAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.01
R work: 0.17897
R free: 0.22163
Average B factor: 43.37
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: CRYSTALS WERE GROWN AT 4C IN 0.1 M BIS-TRIS PROPANE, PH 7.5, CONTAINING 20 % (W/V) POLYETHYLENE GLYCOL 3350, 0.2 M NAI
Matthews coefficient: 2.5
Solvent content (%): 50.8
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: 2016-01-13
Parkin (UblR0RBR) (PDB entry 5C1Z)
Macromolecule: E3 ubiquitin-protein ligase parkin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 405 residues
Sequence: MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQSIVHIVQRPWRKGQEMNATNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAVFEASGTTTQAYRVDERAAEQARWEAASKETIKKTTKPCPRCHVPVEKNGGCMHMKCPQPQCRLEWCWNCGCEWNRVCMGDHWFDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1915
R free: 0.2123
Average B factor: 49.13
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: LiSO4, PEG3350
Matthews coefficient: 2.56
Solvent content (%): 51.9
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: 2015-07-29
Human PARP14 (ARTD8), catalytic fragment in complex with inhibitor H10 (PDB entry 5LYH)
Macromolecule: Poly [ADP-ribose] polymerase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 193 residues
Sequence: SMDMKQQNFCVVELLPSDPEYNTVASKFNQTCSHFRIEKIERIQNPDLWNSYQAKKKTMDAKNGQTMNEKQLFHGTDAGSVPHVNRNGFNRSYAGKNAVAYGKGTYFAVNANYSANDTYSRPDANGRKHVYYVRVLTGIYTHGNHSLIVPPSKNPQNPTDLYDTVTDNVHHPSLFVAFYDYQAYPEYLITFRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.19535
R free: 0.21783
Average B factor: 61.287
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 293
Crystal growth procedure: 22.5% PEG3350, 0.225M Sodium malonate
Matthews coefficient: 2.75
Solvent content (%): 55.21
Ligand: 3-[2-[4-[2-[[4-[(3-aminocarbonylphenyl)amino]-4-oxidanylidene-butanoyl]amino]ethyl]-1,2,3-triazol-1-yl]ethylsulfamoyl]benzoic acid (7B8)
Ligand formula: C24 H27 N7 O7 S
Ligand molecular weight: 557.579
Ligand SMILES: c1cc(cc(c1)NC(=O)CCC(=O)NCCc2cn(nn2)CCNS(=O)(=O)c3cccc(c3)C(=O)O)C(=O)N
Ligand InChI: InChI=1S/C24H27N7O7S/c25-23(34)16-3-1-5-18(13-16)28-22(33)8-7-21(32)26-10-9-19-15-31(30-29-19)12-11-27-39(37,38)20-6-2-4-17(14-20)24(35)36/h1-6,13-15,27H,7-12H2,(H2,25,34)(H,26,32)(H,28,33)(H,35,36)
Release date: 2016-12-21
Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-bound calmodulin and a nicotinamide adenine dinucleotide (NAD+) (PDB entry 8KA0)
Macromolecule: RDTND-RID CBD
Type: Protein, polypeptide(L)
Source organism: Vibrio vulnificus
EC number: 3.4.22
Sequence length: 416 residues
Sequence: GEASHDSAESLVAARAEKVANLYRWLDTDNDVATDKYVPVPGFERVDVDVSDEVKQRMIQSMSGYIEHTDNQVPKDQAEALATLFVESTLDYDWDKRVEFLTKLESYGYSFEAPHAEKSIVSFWSGKNFKQYRDILDNAQTDGKKVVYDIDVKGNAFAIDLNKHLMRWGGLFLDPDNAEQNQLKSSIDAATFSNTGFWSSVYATGAQNDVYVIAEGGVRLGNYFWNVQLPALRQLQREGLVGEIRLLDKPVSEYKDLPADQIGRRLTDAGVAVKVRFDALSHERQAELLADNPDGYKADTLVELDVKLSAIDSMLRESLPFYSLRTERNLLVQEGEEGFEVRSWPGIDGKSKTILLDNPEDAAQQKSIERFILANFDNFEQMPDELFLVDNKVLSHHDGRTRIIAQKEDGAWTYNT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.217
R free: 0.263
Average B factor: 55.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris-HCl (pH 8.5), 32.5% (w/v) PEG 4000 and 0.15 M sodium acetate.
10 mM NAD+ soaking
Matthews coefficient: 2.38
Solvent content (%): 48.25
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2024-07-10
Vanin-1 complexed with Compound 27 (PDB entry 7SLY)
Macromolecule: Pantetheinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.92
Sequence length: 482 residues
Sequence: GSGHHHHHHGSGDYKDDDDKQDTFTAAVYEHAAILPNATLTPVSREEALALMNRNLDILEGAITSAADQGAHIIVTPEDAIYGWNFNRDSLYPYLEDIPDPEVNWIPCNNRNRFGQTPVQERLSCLAKNNSIYVVANIGDKKPCDTSDPQCPPDGRYQYNTDVVFDSQGKLVARYHKQNLFMGENQFNVPKEPEIVTFNTTFGSFGIFTCFDILFHDPAVTLVKDFHVDTIVFPTAWMNVLPHLSAVEFHSAWAMGMRVNFLASNIHYPSKKMTGSGIYAPNSSRAFHYDMKTEEGKLLLSQLDSHPSHSAVVNWTSYASSIEALSSGNKEFKGTVFFDEFTFVKLTGVAGNYTVCQKDLCCHLSYKMSENIPNEVYALGAFDGLHTVEGRYYLQICTLLKCKTTNLNTCGDSAETASTRFEMFSLSGTFGTQYVFPEVLLSENQLAPGEFQVSTDGRLFSLKPTSGPVLTVTLFGRLYEKD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.19
R free: 0.2228
Average B factor: 65.13
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 100 mM MES pH 6.1-6.7, 22-33% PEG-MME-2000, 10 mM TCEP
Matthews coefficient: 2.48
Solvent content (%): 50.36
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: 2022-01-12
Crystal structure of DAPK1 in complex with genistein. (PDB entry 5AUZ)
Macromolecule: Death-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 293 residues
Sequence: MTVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1768
R free: 0.2058
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2 M ammonium sulfate, 0.1 M MES
Matthews coefficient: 1.91
Solvent content (%): 35.57
Ligand: GENISTEIN (GEN)
Ligand formula: C15 H10 O5
Ligand molecular weight: 270.237
Ligand SMILES: c1cc(ccc1C2=COc3cc(cc(c3C2=O)O)O)O
Ligand InChI: InChI=1S/C15H10O5/c16-9-3-1-8(2-4-9)11-7-20-13-6-10(17)5-12(18)14(13)15(11)19/h1-7,16-18H
Release date: 2015-10-07
Crystal structure of TRIM33 PHD-Bromodomain isoform B in complex with H3K9ac histone peptide (PDB entry 5MR8)
Macromolecule: E3 ubiquitin-protein ligase TRIM33
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 194 residues
Sequence: SMDDDPNEDWCAVCQNGGDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIGKPEVEYDCDNLQHSKKGKTAQGLSPVDQRKCERLLLYLYCHELSIEFQEPVPASIPNYYKIIKKPMDLSTVKKKLQKKHSQHYQIPDDFVADVRLIFKNCERFNEADSEVAQAGKAVALYFEDKLTEIYSDRTFAPLP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.2269
R free: 0.2862
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M Tris pH 8.5, 25% PEG3350
Matthews coefficient: 2.37
Solvent content (%): 48.16
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2018-01-17
The effect of modifier structure on the activation of leukotriene A4 hydrolase aminopeptidase activity. (PDB entry 6O5H)
Macromolecule: Leukotriene A-4 hydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 608 residues
Sequence: IVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPDVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.84
R work: 0.2186
R free: 0.2286
Average B factor: 25.759
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295.15
Crystal growth procedure: 50 - 80 mM magnesium formate dihydrate and 24% - 29% PEG3350
Matthews coefficient: 2.29
Solvent content (%): 46.26
Ligand: 4-{4-[(4-methoxyphenyl)methyl]phenyl}-1,3-thiazol-2-amine (LNJ)
Ligand formula: C17 H16 N2 O S
Ligand molecular weight: 296.387
Ligand SMILES: COc1ccc(cc1)Cc2ccc(cc2)c3csc(n3)N
Ligand InChI: InChI=1S/C17H16N2OS/c1-20-15-8-4-13(5-9-15)10-12-2-6-14(7-3-12)16-11-21-17(18)19-16/h2-9,11H,10H2,1H3,(H2,18,19)
Release date: 2019-12-04
The tandem SH2 domains of SYK with a bound FCER1G diphospho-ITAM peptide (PDB entry 7Q5T)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 265 residues
Sequence: SMADSANHLPFFFGNITREEAEDYLVQGGMSDGLYLLRQSRNYLGGFALSVAHGRKAHHYTIERELNGTYAIAGGRTHASPADLCHYHSQESDGLVCLLKKPFNRPQGVQPKTGPFEDLKENLIREYVKQTWNLQGQALEQAIISQKPQLEKLIATTAHEKMPWFHGKISREESEQIVLIGSKTNGKFLIRARDNNGSYALCLLHEGKVLHYRIDKDKTGKLSIPEGKKFDTLWQLVEHYSYKADGLLRVLTVPCQKIGTQGNVN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2075
R free: 0.255
Average B factor: 63.047
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulphate, 100 mM Tris/BICINE, 10% PEG 20,000, 20% PEG 500 MME
Matthews coefficient: 2.37
Solvent content (%): 48.14
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2021-11-24
Crystal structure of MAP2K6 with a covalent compound GCL94 (PDB entry 8PM3)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 290 residues
Sequence: SMEVKADDLEPIMELGRGAYGVVEKMRHVPSGQIMAVKRIRATVNSQEQKRLLMDLDISMRTVDCPFTVTFYGALFREGDVWICMELMDTSLDKFYKQVIDKGQTIPEDILGKIAVSIVKALEHLHSKLSVIHRDVKPSNVLINALGQVKMCDFGISGYLVDDVAKDIDAGCKPYMAPERINPELNQKGYSVKSDIWSLGITMIELAILRFPYDSWGTPFQQLKQVVEEPSPQLPADKFSAEFVDFTSQCLKKNSKERPTYPELMQHPFFTLHESKGTDVASFVKLILGD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1957
R free: 0.23615
Average B factor: 33.296
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.05M magnesium chloride -- 30% PEG500MME -- 0.1M HEPES pH 7.5
Matthews coefficient: 2.57
Solvent content (%): 52.09
Ligand: ~{N}-[3-(2-azanylpyridin-4-yl)phenyl]propanamide (ZLE)
Ligand formula: C14 H15 N3 O
Ligand molecular weight: 241.288
Ligand SMILES: CCC(=O)Nc1cccc(c1)c2ccnc(c2)N
Ligand InChI: InChI=1S/C14H15N3O/c1-2-14(18)17-12-5-3-4-10(8-12)11-6-7-16-13(15)9-11/h3-9H,2H2,1H3,(H2,15,16)(H,17,18)
Release date: 2023-09-20
Crystal structure of human carbonic anhydrase II in complex with Benzoxaborole at pH 7.4 (PDB entry 5JQT)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 262 residues
Sequence: MGMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.36
R work: 0.121
R free: 0.1647
Average B factor: 14.163
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 298
Crystal growth procedure: 2.4 M SODIUM MALONATE
Matthews coefficient: 2.07
Solvent content (%): 40.47
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: 2016-10-19
PRDM9-allele-C ZnF8-13 (PDB entry 5V3G)
Macromolecule: DNA (5'-D(*TP*GP*AP*CP*CP*CP*CP*AP*GP*TP*GP*AP*GP*CP*GP*TP*TP*GP*CP*CP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 21 residues
Sequence: TGACCCCAGTGAGCGTTGCCC
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.416
R work: 0.1731
R free: 0.2254
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 289
Crystal growth procedure: 0.1 M Bis-Tris Propane (pH-7.3) and 23% W/V PEG3350
Matthews coefficient: 2.84
Solvent content (%): 56.7
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: 2017-08-23
STRUCTURE OF INTERFERON LAMBDA 1 RECEPTOR WITH HUMAN KINASE JAK1 (PDB entry 5L04)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 550 residues
Sequence: GAPEPGVEVIFYLSDREPLRLGSGEYTAEELCIRAAQACRISPLCHNLFALYDENTKLWYAPNRTITVDDKMSLRLHYRMRFYFTNWHGTNDNEQSVWRHSPKKQKNGYEKKKIPDATPLLDASSLEYLFAQGQYDLVKCLAPIRDPKTEQDGHDIENECLGMAVLAISHYAMMKKMQLPELPKDISYKRYIPETLNKSIRQRNLLTRMRINNVFKDFLKEFNNKTICDSSVSTHDLKVKYLATLETLTKHYGAEIFETSMLLISSENEMNWFHSNDGGNVLYYEVMVTGNLGIQWRHKPNVVSVEKEKNKLKRKKLENKHKKDEEKNKIREEWNNFSYFPEITHIVIKESVVSINKQDNKKMELKLSSHEEALSFVSLVDGYFRLTADAHHYLCTDVAPPLIVHNIQNGCHGPICTEYAINKLRQEGSEEGMYVLRWSCTDFDNILMTVTCFEKSEQVQGAQKQFKNFQIEVQKGRYSLHGSDRSFPSLGDLMSHLKKQILRTDNISFMLKRCCQPKPREISNLLVATKKAQEWQPVYPMSQLSFDRSG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1687
R free: 0.2304
Average B factor: 50.996
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 7 mg/ml of protein in 50 mM Hepes buffer (pH 7.5) with 150 mM NaCl, mixesd with 1:1 ratio with
18% (w/v) PEG 3350, 0.2 M amonium formate
Matthews coefficient: 2.55
Solvent content (%): 51.73
Release date: 2016-10-12
Crystal structure of MAGEG1 and NSE1 complex (PDB entry 5WY5)
Macromolecule: Melanoma-associated antigen G1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 217 residues
Sequence: GPRSQKQLELKVSELVQFLLIKDQKKIPIKRADILKHVIGDYKDIFPDLFKRAAERLQYVFGYKLVELEPKSNTYILINTLEPVEEDAEMRGDQGTPTTGLLMIVLGLIFMKGNTLKETEAWDFLRRLGVYPTKKHLIFGDPKKLITEDFVRQRYLEYRRIPHTDPVDYEFQWGPRTNLELSKMKVLKFVAKVHNQDPKDWPAQYCEALADEENRAR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.92
R work: 0.216
R free: 0.27
Crystallization method: EVAPORATION
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 22%(V/V) PEG 500, 0.1M SODIUM CITRATR
 PH5.5, 2%(V/V) 1,1,1,3,3,3-HEXAFLUORO-2-PROPANOL, VAPOR
 DIFFUSION, HANGING DROP, TEMPERATURE 291K
Matthews coefficient: 3.25
Solvent content (%): 62.14
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2017-05-03
Notum Fragment_130 (4H-thieno[3,2-c]chromene-2-carboxylic acid) (PDB entry 7BO2)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 382 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.21
R work: 0.1991
R free: 0.2194
Average B factor: 16.9047
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 2.01
Solvent content (%): 38.71
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: 2022-03-02
Crystal structure of Aldo-keto reductase 1C3 complexed with compound S07054 (PDB entry 7X3O)
Macromolecule: Aldo-keto reductase family 1 member C3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 329 residues
Sequence: MHHHHHHDSKHQCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKKAQLDYVDLYLIHSPMSLKPGEELSPTDENGKVIFDIVDLCTTWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHYFNSDSFASHPNYPYSDEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.001
R work: 0.1981
R free: 0.2379
Average B factor: 23.2394
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: MES pH 6.0, Ammonium chloride, PEG 6000
Matthews coefficient: 2.43
Solvent content (%): 49.3
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: 2023-03-08