satarupa22/MacromolecularLigandDB huggingface dataset:
Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) Bound to AMPPNP (PDB entry 4U40)
Macromolecule: Mitogen-activated protein kinase kinase kinase kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 332 residues
Sequence: GSANDSPAKSLVDIDLSSLRDPAGIFELVEVVGNGTYGQVYKGRHVKTGQLAAIKVMDVTEDEEEEIKLEINMLKKYSHHRNIATYYGAFIKKSPPGHDDQLWLVMEFCGAGSITDLVKNTKGNTLKEDWIAYISREILRGLAHLHIHHVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATYDYRSDLWSCGITAIEMAEGAPPLCDMHPMRALFLIPRNPPPRLKSKKWSKKFFSFIEGCLVKNYMQRPSTEQLLKHPFIRDQPNERQVRIQLKDHIDRTRKKRGEKDETEYEYSGSEEGNS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1983
R free: 0.2615
Average B factor: 56.5528
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 292
Crystal growth procedure: 0.2 M potassium citrate, pH 8.3, 20% PEG 3350
Matthews coefficient: 2.12
Solvent content (%): 42.1
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2016-01-06
Crystal structure of TTK kinase domain in complex with compound 30 (PDB entry 7CHT)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 282 residues
Sequence: NECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2096
R free: 0.2587
Average B factor: 75.15
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 294.15
Crystal growth procedure: 7-9% PEG 10000,  0.08-0.14 M magnesium acetate, 0.1 M MES pH 6.0
Matthews coefficient: 3.29
Solvent content (%): 62.58
Ligand: 2-[[2-methoxy-4-(2-oxidanylidenepyrrolidin-1-yl)phenyl]amino]-4-(oxan-4-ylamino)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile (FZO)
Ligand formula: C23 H25 N7 O3
Ligand molecular weight: 447.49
Ligand SMILES: COc1cc(ccc1Nc2nc3c(c(c[nH]3)C#N)c(n2)NC4CCOCC4)N5CCCC5=O
Ligand InChI: InChI=1S/C23H25N7O3/c1-32-18-11-16(30-8-2-3-19(30)31)4-5-17(18)27-23-28-21-20(14(12-24)13-25-21)22(29-23)26-15-6-9-33-10-7-15/h4-5,11,13,15H,2-3,6-10H2,1H3,(H3,25,26,27,28,29)
Release date: 2021-05-12
Crystal structure of Tdp1 catalytic domain in complex with Sigma Aldrich compound CDS010292 (PDB entry 6DJE)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.705
R work: 0.1913
R free: 0.2271
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: .1 M MOPS/HEPES-Na pH 7.5
10% w/v PEG 8000
20% v/v ethylene glycol
0.03M sodium fluoride
0.03M sodium bromide
0.03M sodium iodide
Matthews coefficient: 2.46
Solvent content (%): 50.02
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: 2019-05-29
CRYSTAL STRUCTURE OF SPLEEN TYROSINE KINASE (SYK) IN COMPLEX WITH A 2-(PHENOXYMETHYL)PYRIDINE INHIBITOR (PDB entry 6HM7)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 276 residues
Sequence: PKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.172
R free: 0.2101
Average B factor: 27.959
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, bistrispropane, sodium bromide
Matthews coefficient: 2.16
Solvent content (%): 43.04
Ligand: BROMIDE ION (BR)
Ligand formula: Br
Ligand molecular weight: 79.904
Ligand SMILES: [Br-]
Ligand InChI: InChI=1S/BrH/h1H/p-1
Release date: 2018-10-10
Binary complex crystal structure of DNA polymerase Beta with T:C mismatch at the primer terminus (PDB entry 5J0W)
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): 2.4
R work: 0.2344
R free: 0.3064
Average B factor: 29.2081
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: 2.4
Solvent content (%): 48.83
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 the human Bub1 kinase domain in complex with BAY 1816032 (PDB entry 6F7B)
Macromolecule: Mitotic checkpoint serine/threonine-protein kinase BUB1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 361 residues
Sequence: GSSLGTVDAPNFIVGNPWDDKLIFKLLSGLSKPVSSYPNTFEWQCKLPAIKPKTEFQLGSKLVYVHHLLGEGAFAQVYEATQGDLNDAKNKQKFVLKVQKPANPWEFYIGTQLMERLKPSMQHMFMKFYSAHLFQNGSVLVGELYSYGTLLNAINLYKNTPEKVMPQGLVISFAMRMLYMIEQVHDCEIIHGDIKPDNFILGNGFLEQDDEDDLSAGLALIDLGQSIDMKLFPKGTIFTAKCETSGFQCVEMLSNKPWNYQIDYFGVAATVYCMLFGTYMKVKNEGGECKPEGLFRRLPHLDMWNEFFHVMLNIPDCHHLPSLDLLRQKLKKVFQQHYTNKIRALRNRLIVLLLECKRSRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.19831
R free: 0.25374
Average B factor: 40.779
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.26
Crystallization temperature (K): 277
Crystal growth procedure: 200mM MgCl2, 100mM Tris-HCl pH 7.26, 5% glycerol, 20% PEG 3350
Matthews coefficient: 2.28
Solvent content (%): 45.96
Ligand: 2-[3,5-bis(fluoranyl)-4-[[3-[5-methoxy-4-[(3-methoxypyridin-4-yl)amino]pyrimidin-2-yl]indazol-1-yl]methyl]phenoxy]ethanol (CVQ)
Ligand formula: C27 H24 F2 N6 O4
Ligand molecular weight: 534.514
Ligand SMILES: COc1cnccc1Nc2c(cnc(n2)c3c4ccccc4n(n3)Cc5c(cc(cc5F)OCCO)F)OC
Ligand InChI: InChI=1S/C27H24F2N6O4/c1-37-23-13-30-8-7-21(23)32-26-24(38-2)14-31-27(33-26)25-17-5-3-4-6-22(17)35(34-25)15-18-19(28)11-16(12-20(18)29)39-10-9-36/h3-8,11-14,36H,9-10,15H2,1-2H3,(H,30,31,32,33)
Release date: 2018-12-19
Crystal structure of Human SUMO E2-conjugating enzyme (Ubc9) in complex with E1-activating enzyme (Uba2) ubiquitin fold domain (Ufd) (PDB entry 4W5V)
Macromolecule: SUMO-conjugating enzyme UBC9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 163 residues
Sequence: GPLGSMSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2211
R free: 0.2828
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, pH 8.0, 20% PEG MME 550,
200 mM potassium formate, 20% glycerol; seeded
Matthews coefficient: 2.61
Solvent content (%): 52.8
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: 2015-09-09
Surface Lysine Acetylated Human Carbonic Anhydrase II in Complex with a Sulfamate-Based Inhibitor (PDB entry 4ZWI)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1789
R free: 0.2247
Average B factor: 20.7386
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-HCl, pH 7.8
Matthews coefficient: 2.1
Solvent content (%): 41.51
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: 2015-08-26
Crystal Structure of KRAS4b (GMPPNP-bound) in complex with the RBD-PH domains of SIN1 (PDB entry 7LC1)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGAGGVGKSALTIQLIANHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.2314
R free: 0.2792
Average B factor: 70.2582
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 200 mM ammonium sulfate, 100 mM HEPES (N-2-hydroxyethyl piperazine-N-ethane sulfonic acid) pH 7.5, 25% PEG 3350
Matthews coefficient: 2.17
Solvent content (%): 43.23
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: 2021-08-04
Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin (PDB entry 6J8F)
Macromolecule: Small vasohibin-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 46 residues
Sequence: PPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.283
R work: 0.1995
R free: 0.2369
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M Na citrate tribasic dihydrate pH 5.0, 18% PEG 20000
Matthews coefficient: 2.5
Solvent content (%): 50.85
Release date: 2019-06-19
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 3e (PDB entry 5NKH)
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): 1.29
R work: 0.17
R free: 0.196
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 37.5% MPD/PEG1000/PEG3350 (MD), 0.1 M Amino Acids Mix (MD), 0.1 M Buffer System 3 (MD) pH8.5
Matthews coefficient: 1.96
Solvent content (%): 37.29
Ligand: 2-[[3-(2-aminophenyl)-5-(piperidin-4-ylcarbamoyl)phenyl]amino]-~{N}-(2-chloranyl-6-methyl-phenyl)-1,3-thiazole-5-carboxamide (8ZQ)
Ligand formula: C29 H29 Cl N6 O2 S
Ligand molecular weight: 561.098
Ligand SMILES: Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cc(cc(c3)C(=O)NC4CCNCC4)c5ccccc5N)Cl
Ligand InChI: InChI=1S/C29H29ClN6O2S/c1-17-5-4-7-23(30)26(17)36-28(38)25-16-33-29(39-25)35-21-14-18(22-6-2-3-8-24(22)31)13-19(15-21)27(37)34-20-9-11-32-12-10-20/h2-8,13-16,20,32H,9-12,31H2,1H3,(H,33,35)(H,34,37)(H,36,38)
Release date: 2017-06-07
Crystal structure of double tudor domain of human lysine demethylase KDM4A (PDB entry 5D6X)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 121 residues
Sequence: GSHMALQSITAGQKVISKHKNGRFYQCEVVRLTTETFYEVNFDDGSFSDNLYPEDIVSQDCLQFGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQVEFEDGSQLVVKRDDVYTLDEELP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.153
R work: 0.1586
R free: 0.1997
Average B factor: 37.2003
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Protein Solution (30mg/ml KDM4A DTD, 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.0M ammonium sulfate, 1% w/v peg3350 and 0.1M Bis-Tris pH5.5) Cryoprotected with additional 20% glycerol
Matthews coefficient: 3.72
Solvent content (%): 66.93
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: 2015-11-25
Protein Tyrosine Phosphatase 1B (1-301), F182A mutant, vanadate bound state (PDB entry 6PHA)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 297 residues
Sequence: EMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDAGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.299
R work: 0.2241
R free: 0.2765
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Hepes,  0.2 M magnesium acetate and 15-20% polyethylene glycol 8000
Matthews coefficient: 3.28
Solvent content (%): 62.53
Ligand: VANADATE ION (VO4)
Ligand formula: O4 V
Ligand molecular weight: 114.939
Ligand SMILES: [O-][V](=O)([O-])[O-]
Ligand InChI: InChI=1S/4O.V/q;3*-1;
Release date: 2019-08-07
Crystal structure of CDK2 in complex with 2,4,6-trioxo-1-phenyl- hexahydropyrimidine-5-carboxamide processed with the CrystalDirect automated mounting and cryo-cooling technology (PDB entry 5ANK)
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): 1.9
R work: 0.19488
R free: 0.2359
Average B factor: 48.579
Crystal growth procedure: 0.02 M HEPES, PH=7.0, 5% GLYCEROL, 12% PEG 3350
Matthews coefficient: 1.87
Solvent content (%): 34.33
Ligand: 2,4,6-TRIOXO-1-PHENYL-HEXAHYDROPYRIMIDINE-5-CARBOXAMIDE (RJI)
Ligand formula: C11 H9 N3 O4
Ligand molecular weight: 247.207
Ligand SMILES: c1ccc(cc1)N2C(=O)C(C(=O)NC2=O)C(=O)N
Ligand InChI: InChI=1S/C11H9N3O4/c12-8(15)7-9(16)13-11(18)14(10(7)17)6-4-2-1-3-5-6/h1-5,7H,(H2,12,15)(H,13,16,18)/t7-/m0/s1
Release date: 2016-04-13
Crystal structure of human Cathepsin K with a non-active site inhibitor at 1.42 Angstrom resolution (PDB entry 6ASH)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 215 residues
Sequence: APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLAPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.423
R work: 0.1158
R free: 0.1463
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 295
Crystal growth procedure: 8% polyethylene glycol (PEG) 4000, 0.1 M sodium acetate
Matthews coefficient: 2.23
Solvent content (%): 44.85
Ligand: 2-{[(carbamoylsulfanyl)acetyl]amino}benzoic acid (1XF)
Ligand formula: C10 H10 N2 O4 S
Ligand molecular weight: 254.262
Ligand SMILES: c1ccc(c(c1)C(=O)O)NC(=O)CSC(=O)N
Ligand InChI: InChI=1S/C10H10N2O4S/c11-10(16)17-5-8(13)12-7-4-2-1-3-6(7)9(14)15/h1-4H,5H2,(H2,11,16)(H,12,13)(H,14,15)
Release date: 2018-08-29
Crystal structure of the tandem bromodomain (BD1, BD2) of human TAF1 bound to ZS1-585 (PDB entry 7LB1)
Macromolecule: Transcription initiation factor TFIID subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 265 residues
Sequence: SMSIHRRRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELESLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.1632
R free: 0.1795
Average B factor: 27.0521
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.15 M MgCl2, 0.1 M Bis-Tris pH 5.5, 15% PEG 3350
Matthews coefficient: 2.57
Solvent content (%): 52.22
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: 2021-07-14
COAGULATION FACTOR XI CATALYTIC DOMAIN (C123S) IN COMPLEX WITH NVP-XIV936 (PDB entry 6USY)
Macromolecule: Coagulation factor XIa light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 238 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.26
R work: 0.166
R free: 0.188
Average B factor: 19.62
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bit-Tris pH 7.0, 0.6 M NaCl, 25 % (w/v) PEG3,350
Matthews coefficient: 2.3
Solvent content (%): 46.57
Ligand: 1-[(2S)-2-{3-[(3S)-3-amino-2,3-dihydro-1-benzofuran-5-yl]-5-(propan-2-yl)phenyl}-2-hydroxyethyl]-1H-indole-7-carboxylic acid (QGS)
Ligand formula: C28 H28 N2 O4
Ligand molecular weight: 456.533
Ligand SMILES: CC(C)c1cc(cc(c1)C(Cn2ccc3c2c(ccc3)C(=O)O)O)c4ccc5c(c4)C(CO5)N
Ligand InChI: InChI=1S/C28H28N2O4/c1-16(2)19-10-20(18-6-7-26-23(13-18)24(29)15-34-26)12-21(11-19)25(31)14-30-9-8-17-4-3-5-22(27(17)30)28(32)33/h3-13,16,24-25,31H,14-15,29H2,1-2H3,(H,32,33)/t24-,25-/m1/s1
Release date: 2020-07-01
DISCOVERY OF NOVEL 7-AZAINDOLES AS PDK1 INHIBITORS (PDB entry 5HO8)
Macromolecule: 3-phosphoinositide-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 309 residues
Sequence: MDGTAAEPRPGAGSLQHAQPPPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEYLIFQKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.182
R free: 0.229
Average B factor: 55.18
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.6
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM Tris-HCl, 1.8 M NH4-sulfate
Matthews coefficient: 2.91
Solvent content (%): 57.71
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: 2016-06-08
Crystal structure of PDE5A in complex with inhibitor L1 (PDB entry 7FAQ)
Macromolecule: cGMP-specific 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.35
Sequence length: 349 residues
Sequence: SYHASAAEEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQEKMLINGESGQAKRN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.20013606546
R work: 0.225164311103
R free: 0.272067669888
Average B factor: 49.9247361213
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M magnesium sulfate, 0.1 M sodium cacodylate, pH 6.5, 17% PEG3350
Matthews coefficient: 2.58
Solvent content (%): 52.32
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2022-05-18