satarupa22/MacromolecularLigandDB huggingface dataset:
CRYSTAL STRUCTURE OF TIE2 IN COMPLEX WITH DECIPERA COMPOUND DP1919 (PDB entry 6MWE)
Macromolecule: Angiopoietin-1 receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 317 residues
Sequence: KNNPDPTIYPVLDWNDIKFQDVIGEGNFGQVLKARIKKDGLRMDAAIKRMKEYASKDDHRDFAGELEVLCKLGHHPNIINLLGACEHRGYLYLAIEYAPHGNLLDFLRKSRVLETDPAFAIANSTASTLSSQQLLHFAADVARGMDYLSQKQFIHRDLAARNILVGENYVAKIADFGLSRGQEVYVKKTMGRLPVRWMAIESLNYSVYTTNSDVWSYGVLLWEIVSLGGTPYCGMTCAELYEKLPQGYRLEKPLNCDDEVYDLMRQCWREKPYERPSFAQILVSLNRMLEERKTYVNTTLYEKFTYAGIDCSAEEAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.148
R free: 0.166
Average B factor: 36.96
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 290
Crystal growth procedure: JCSG+ screen e4: 1.26M ammonium sulphate: 200mM lithium sulphate, 100mM Tris pH 8.5: cryo: 25% EG in 3 steps
Matthews coefficient: 2.5
Solvent content (%): 51
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: 2018-11-21
Structure of LRRK2-CHK1 10-pt. mutant complex with heteroaryl-1H-indazole LRRK2 inhibitor 25 (PDB entry 8E81)
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): 1.62
R work: 0.2
R free: 0.232
Average B factor: 31.99
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 11% PEG 8000, 15-20% ethylene glycol, 0.1 M MES (pH 6.5), 5% 6-aminohexanoic acid
Matthews coefficient: 2.37
Solvent content (%): 48.02
Ligand: (1S)-1-[(1P)-1-{6-[(3R)-3-(2-hydroxypropan-2-yl)pyrrolidin-1-yl]pyrimidin-4-yl}-1H-indazol-6-yl]spiro[2.2]pentane-1-carbonitrile (UU6)
Ligand formula: C24 H26 N6 O
Ligand molecular weight: 414.503
Ligand SMILES: CC(C)(C1CCN(C1)c2cc(ncn2)n3c4cc(ccc4cn3)C5(CC56CC6)C#N)O
Ligand InChI: InChI=1S/C24H26N6O/c1-22(2,31)18-5-8-29(12-18)20-10-21(27-15-26-20)30-19-9-17(4-3-16(19)11-28-30)24(14-25)13-23(24)6-7-23/h3-4,9-11,15,18,31H,5-8,12-13H2,1-2H3/t18-,24-/m1/s1
Release date: 2023-02-22
Carbonic Anhydrase II Inhibitor RA7 (PDB entry 5NXP)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 258 residues
Sequence: HHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.1282
R free: 0.1623
Average B factor: 17.478
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Tris
1.6 M Natrium Citrate
Matthews coefficient: 2.05
Solvent content (%): 40
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 X-ray co-crystal structure of human CDK6 and Abemaciclib. (PDB entry 5L2S)
Macromolecule: Cyclin-dependent kinase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 307 residues
Sequence: MEKDGLCRADQQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVQTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDRETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLDFLHSHRVVHRDLKPQNILVTSSGQIKLADFGLARIYSFQMALTSVVVTLWYRAPEVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILDVIGLPGEEDWPRDVALPRQAFHSKSAQPIEKFVTDIDELGKDLLLKCLTFNPAKRISAYSALSHPYFQHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.27
R work: 0.206
R free: 0.2488
Average B factor: 58.77
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 286.15
Crystal growth procedure: 1:1 (protein to well buffer) with well buffer containing:  0.1 M MES pH 6.0, 70 - 80 mM NH4NO3, 10 - 15% polyethyleneglycol 3350
Matthews coefficient: 2.28
Solvent content (%): 46.13
Ligand: N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-benzimidazol-6-yl]py
rimidin-2-amine (6ZV)
Ligand formula: C27 H32 F2 N8
Ligand molecular weight: 506.593
Ligand SMILES: CCN1CCN(CC1)Cc2ccc(nc2)Nc3ncc(c(n3)c4cc5c(c(c4)F)nc(n5C(C)C)C)F
Ligand InChI: InChI=1S/C27H32F2N8/c1-5-35-8-10-36(11-9-35)16-19-6-7-24(30-14-19)33-27-31-15-22(29)25(34-27)20-12-21(28)26-23(13-20)37(17(2)3)18(4)32-26/h6-7,12-15,17H,5,8-11,16H2,1-4H3,(H,30,31,33,34)
Release date: 2016-08-24
Binary complex crystal structure of DNA polymerase Beta with C:T mismatch at the primer terminus (PDB entry 5J0S)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1987
R free: 0.2455
Average B factor: 25.4648
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
Matthews coefficient: 2.44
Solvent content (%): 49.54
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2016-10-26
Crystal structure of CDK2 liganded with compound WN333 (PDB entry 7RXO)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.38
R work: 0.2203
R free: 0.2332
Average B factor: 31.0359
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 4.5mg/mL of CDK2 protein crystalized in 50mM sodium/potassium phosphate, 50mM Hepes Na, pH 7.5, 7.5%PEG3350, then soak in 1mM WN333 for 48hours at 0.1M Hepes Na, pH7.5, 15%PEG3350
Matthews coefficient: 2.08
Solvent content (%): 40.82
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: 2022-08-31
Anaerobic crystal structure of apo-HIF prolyl hydroxylase 2 (PHD2 181-407)in complex with acetate (ACT) and HIF2alpha-CODD peptide (PDB entry 8Q5S)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 233 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.1892
R free: 0.213
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: (10-35%) PEG 4K, 0.2 M ammonium acetate, 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6)
Matthews coefficient: 1.86
Solvent content (%): 34.1
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: 2024-08-21
Crystal structure of domain I10 from titin (space group P41) (PDB entry 4QEG)
Macromolecule: Titin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 91 residues
Sequence: GAMETLHITKTMKNIEVPETKTASFECEVSHFNVPSMWLKNGVEIEMSEKFKIVVQGKLHQLIIMNTSTEDSAEYTFVCGNDQVSATLTVT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1834
R free: 0.2312
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystal growth procedure: 0.2 M CaCl2, 30% PEG 3350, 0.1 M Tris, 3% Isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP
Matthews coefficient: 2.25
Solvent content (%): 45.31
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: 2015-07-22
Minimal construct of Cdc7-Dbf4 bound to XL413 (PDB entry 6YA6)
Macromolecule: Protein DBF4 homolog A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 144 residues
Sequence: GPGTRTGRLKKPFVKVEDMSQLYRPFYLQLTNMPFINYSIQKPCSPFDVDKPSSMQKQTQVKLRIQTDGDKYGGTSIQLQLKEKKKKGYCECCLQKYEDLETHLLSEQHRNFAQSNQYQVVDDIVSKLVFDFVEYEKDTPKKKR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.1666
R free: 0.1933
Average B factor: 20.95
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1M PCTP pH7, 18% PEG 1500, 8% MPD
Matthews coefficient: 2.15
Solvent content (%): 42.72
Ligand: 8-chloro-2-[(2S)-pyrrolidin-2-yl][1]benzofuro[3,2-d]pyrimidin-4(3H)-one (0SX)
Ligand formula: C14 H12 Cl N3 O2
Ligand molecular weight: 289.717
Ligand SMILES: c1cc2c(cc1Cl)c3c(o2)C(=O)NC(=N3)C4CCCN4
Ligand InChI: InChI=1S/C14H12ClN3O2/c15-7-3-4-10-8(6-7)11-12(20-10)14(19)18-13(17-11)9-2-1-5-16-9/h3-4,6,9,16H,1-2,5H2,(H,17,18,19)/t9-/m0/s1
Release date: 2020-05-27
RNF12 RING domain in complex with Ube2d2 (PDB entry 6W7Z)
Macromolecule: E3 ubiquitin-protein ligase RLIM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 99 residues
Sequence: GPLGSLAQFFLLNEDDDDQPRGLTKEQIDNLAMRSFGENDALKTCSVCITEYTEGNKLRKLPCSHEYHVHCIDRWLSENSTCPICRRAVLASGNRESVV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1779
R free: 0.2108
Average B factor: 34.9294
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 15-20% PEG 3350, 100-200 mM ammonium formate
Matthews coefficient: 2.4
Solvent content (%): 49
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: 2020-05-20
X-RAY STRUCTURE OF MPS1 IN COMPLEX WITH COMPOUND 41 (PDB entry 6TNB)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 294 residues
Sequence: GSNECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2124
R free: 0.2616
Average B factor: 80.611
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.54
Crystallization temperature (K): 293
Crystal growth procedure: 1.2M Ammonium sulphate, 100mM sodium cacodylate pH 6.54m 25% glycerol
Matthews coefficient: 3.64
Solvent content (%): 66.23
Ligand: (2~{R})-2-(4-fluorophenyl)-~{N}-[4-[2-[(2-methoxy-4-methylsulfonyl-phenyl)amino]-[1,2,4]triazolo[1,5-a]pyridin-6-yl]phenyl]propanamide (8QW)
Ligand formula: C29 H26 F N5 O4 S
Ligand molecular weight: 559.611
Ligand SMILES: CC(c1ccc(cc1)F)C(=O)Nc2ccc(cc2)c3ccc4nc(nn4c3)Nc5ccc(cc5OC)S(=O)(=O)C
Ligand InChI: InChI=1S/C29H26FN5O4S/c1-18(19-4-9-22(30)10-5-19)28(36)31-23-11-6-20(7-12-23)21-8-15-27-33-29(34-35(27)17-21)32-25-14-13-24(40(3,37)38)16-26(25)39-2/h4-18H,1-3H3,(H,31,36)(H,32,34)/t18-/m1/s1
Release date: 2020-05-13
Fluorine substituted 5-methyl-6-(3',4'-difluoromethoxyphenythio)thieno[2,3-d]pyrimidine-2,4-diamine (PDB entry 5HSR)
Macromolecule: Dihydrofolate reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.3
Sequence length: 186 residues
Sequence: VGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.21
R work: 0.19323
R free: 0.21903
Average B factor: 16.748
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 287
Crystal growth procedure: 100 mM KPO4, pH 6.9, 60% sat AmSO4, 3% v/v ETOH
Matthews coefficient: 2.52
Solvent content (%): 51.18
Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NDP)
Ligand formula: C21 H30 N7 O17 P3
Ligand molecular weight: 745.421
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
Ligand InChI: InChI=1S/C21H30N7O17P3/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/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2017-02-01
2-[2-(4-Phenyl-1H-imidazol-2-yl)ethyl]quinoxaline (Sunovion Compound 14) co-crystallized with PDE10A (PDB entry 4YQH)
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: 321 residues
Sequence: SICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGE
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.308
R work: 0.2362
R free: 0.3007
Average B factor: 55.643
Crystallization method: BATCH MODE
Crystallization temperature (K): 291
Crystal growth procedure: magnesium chloride, PEG3350
Matthews coefficient: 2.2
Solvent content (%): 43.97
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: 2015-04-29
Human VKOR with Brodifacoum (PDB entry 6WVH)
Macromolecule: Vitamin K epoxide reductase, termini restrained by green fluorescent protein
Type: Protein, polypeptide(L)
Source organism: Aequorea victoria
EC number: 1.17.4.4
Sequence length: 390 residues
Sequence: MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNSTWGSPGWVRLALCLTGLVLSLYALHVKAARARDRDYRALCDVGTAISCSRVFSSRWGRGFGLVEHVLGQDSILNQSNSIFGCIFYTLQLLLGCLRTRWASVLMLLSSLVSLAGSVYLAWILFFVLYDFCIVCITTYAINVSLMWLSFRKVQENSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.1946
R free: 0.215
Average B factor: 29.69
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 32% PEG400, 0.1 M ammonium acetate, 1% 1,2,3-heptanetriol, 0.1 M MES, pH 6.5
Matthews coefficient: 3.03
Solvent content (%): 59.45
Ligand: Brodifacoum (UA7)
Ligand formula: C31 H23 Br O3
Ligand molecular weight: 523.417
Ligand SMILES: c1ccc2c(c1)CC(CC2C3=C(c4ccccc4OC3=O)O)c5ccc(cc5)c6ccc(cc6)Br
Ligand InChI: InChI=1S/C31H23BrO3/c32-24-15-13-20(14-16-24)19-9-11-21(12-10-19)23-17-22-5-1-2-6-25(22)27(18-23)29-30(33)26-7-3-4-8-28(26)35-31(29)34/h1-16,23,27,33H,17-18H2/t23-,27-/m1/s1
Release date: 2020-11-11
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1575337975 (PDB entry 7G94)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47
R work: 0.1914
R free: 0.2244
Average B factor: 32.17
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 (%): 50.65
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
Strategic design of catalytic lysine-targeting reversible covalent BCR-ABL Inhibitors (PDB entry 7CC2)
Macromolecule: Tyrosine-protein kinase ABL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 310 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMENLYFQSSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.723
R work: 0.1922
R free: 0.2418
Average B factor: 46.1251
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 7 % w/v Polyethylene glycol 8000, 100 mM MES pH 6.5, 20 % v/v Ethylene glycol
Matthews coefficient: 2.93
Solvent content (%): 57.98
Ligand: [4-[5-[5-(dimethylcarbamoyl)pyridin-3-yl]-1H-pyrrolo[2,3-b]pyridin-3-yl]-2-methyl-phenyl]boronic acid (FVC)
Ligand formula: C22 H21 B N4 O3
Ligand molecular weight: 400.238
Ligand SMILES: B(c1ccc(cc1C)c2c[nH]c3c2cc(cn3)c4cc(cnc4)C(=O)N(C)C)(O)O
Ligand InChI: InChI=1S/C22H21BN4O3/c1-13-6-14(4-5-20(13)23(29)30)19-12-26-21-18(19)8-16(11-25-21)15-7-17(10-24-9-15)22(28)27(2)3/h4-12,29-30H,1-3H3,(H,25,26)
Release date: 2021-06-09
CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN (UNTREATED) IN COMPLEX WITH SARACATINIB (PDB entry 5VCX)
Macromolecule: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 311 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMHQLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2013
R free: 0.2436
Average B factor: 54.6016
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000, 1 mM SARACATINIB
Matthews coefficient: 2.46
Solvent content (%): 49.98
Ligand: N-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-7-[2-(4-METHYLPIPERAZIN-1-YL)ETHOXY]-5-(TETRAHYDRO-2H-PYRAN-4-YLOXY)QUINAZOLIN-4-AMINE (H8H)
Ligand formula: C27 H32 Cl N5 O5
Ligand molecular weight: 542.026
Ligand SMILES: CN1CCN(CC1)CCOc2cc3c(c(c2)OC4CCOCC4)c(ncn3)Nc5c(ccc6c5OCO6)Cl
Ligand InChI: InChI=1S/C27H32ClN5O5/c1-32-6-8-33(9-7-32)10-13-35-19-14-21-24(23(15-19)38-18-4-11-34-12-5-18)27(30-16-29-21)31-25-20(28)2-3-22-26(25)37-17-36-22/h2-3,14-16,18H,4-13,17H2,1H3,(H,29,30,31)
Release date: 2017-08-23
Crystal Structure of human phosphodiesterase 10 in complex with 2-methyl-4-(morpholine-4-carbonyl)-N-(2-phenylimidazo[1,2-a]pyridin-7-yl)pyrazole-3-carboxamide, space group H3 (PDB entry 5SK5)
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): 1.95
R work: 0.1893
R free: 0.2217
Average B factor: 35.436
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: 2.63
Solvent content (%): 53.18
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: 2022-10-12