satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of EGFR T790M/V948R in Complex with Covalent Pyrrolopyrimidine 18c (PDB entry 6TFY)
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): 1.7
R work: 0.1923
R free: 0.2119
Average B factor: 42.3012
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30 % PEG3350, 100 mM MgSO4, 3 % ethylen glycole 7.0 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: 2.32
Solvent content (%): 47.08
Ligand: ~{N}-[5-[4-[[3-chloranyl-4-(pyridin-2-ylmethoxy)phenyl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]-2-(3-oxidanylpropoxy)phenyl]propanamide (N7Z)
Ligand formula: C30 H29 Cl N6 O4
Ligand molecular weight: 573.042
Ligand SMILES: CCC(=O)Nc1cc(ccc1OCCCO)c2c[nH]c3c2c(ncn3)Nc4ccc(c(c4)Cl)OCc5ccccn5
Ligand InChI: InChI=1S/C30H29ClN6O4/c1-2-27(39)37-24-14-19(7-9-26(24)40-13-5-12-38)22-16-33-29-28(22)30(35-18-34-29)36-20-8-10-25(23(31)15-20)41-17-21-6-3-4-11-32-21/h3-4,6-11,14-16,18,38H,2,5,12-13,17H2,1H3,(H,37,39)(H2,33,34,35,36)
Release date: 2020-09-30
Crystal structure of the EGFR kinase domain mutant I682Q (PDB entry 5CNN)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 350 residues
Sequence: GAMGEAPNQALLRQLKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGFFSSPSTSRTPLLSSLSATS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.182
R free: 0.2114
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: PEG 6000, morpholineethanesulfonic acid, ammonium chloride
Matthews coefficient: 2.5
Solvent content (%): 50.74
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: 2015-07-29
Crystal structure of SYK kinase in complex with compound 1 (PDB entry 8RRZ)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 282 residues
Sequence: GPEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1802
R free: 0.2145
Average B factor: 27.308
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG 3350, 0.1 M bis tris propane pH 6.5, 0.2 M Na formate
Matthews coefficient: 2.09
Solvent content (%): 41.03
Ligand: N-[(2S)-1-(azetidin-1-yl)propan-2-yl]-3-{2-[(3,5-dimethoxyphenyl)amino]pyrimidin-4-yl}-1-methyl-1H-pyrazole-5-carboxamide (A1H2Y)
Ligand formula: C23 H29 N7 O3
Ligand molecular weight: 451.521
Ligand SMILES: CC(CN1CCC1)NC(=O)c2cc(nn2C)c3ccnc(n3)Nc4cc(cc(c4)OC)OC
Ligand InChI: InChI=1S/C23H29N7O3/c1-15(14-30-8-5-9-30)25-22(31)21-13-20(28-29(21)2)19-6-7-24-23(27-19)26-16-10-17(32-3)12-18(11-16)33-4/h6-7,10-13,15H,5,8-9,14H2,1-4H3,(H,25,31)(H,24,26,27)/t15-/m0/s1
Release date: 2024-04-24
PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with RZ373 (PDB entry 5QXU)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYRTVIKEPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1704
R free: 0.1958
Average B factor: 27.491
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 1.6M Ammonium Sulfate, 0.1M bis-tris pH 5.5
Matthews coefficient: 4.2
Solvent content (%): 70.7
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: 2020-04-08
Derivative of mouse TGF-beta2, with a deletion of residues 52-71 and K25R, R26K, L51R, A74K, C77S, L89V, I92V, K94R T95K, I98V single amino acid substitutions, bound to human TGF-beta type II receptor ectodomain residues 15-130 (PDB entry 5TX4)
Macromolecule: TGF-beta receptor type-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 116 residues
Sequence: VTDNNGAVKFPQLCKFCDVRFSTCDNQKSCMSNCSITSICEKPQEVCVAVWRKNDENITLETVCHDPKLPYHDFILEDAASPKCIMKEKKKPGETFFMCSCSSDECNDNIIFSEEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.876
R work: 0.1935
R free: 0.2222
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Hepes, pH 7.5, 60 % v/v (+/-)-2-Methyl-2,4-pentanediol
Matthews coefficient: 2.24
Solvent content (%): 45.18
Release date: 2017-03-01
FACTOR VIIA IN COMPLEX WITH THE INHIBITOR 7-chloro-3,4-dihydroisoquinolin-1(2H)-one (PDB entry 4X8T)
Macromolecule: Factor VIIa (Heavy Chain)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 254 residues
Sequence: IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1978
R free: 0.2212
Average B factor: 39.71
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES, pH 6.0, 20 mM CACL2, 17.5%(W/V) PEG 6000
Matthews coefficient: 3.53
Solvent content (%): 65.19
Ligand: 7-chloro-3,4-dihydroisoquinolin-1(2H)-one (3Z8)
Ligand formula: C9 H8 Cl N O
Ligand molecular weight: 181.619
Ligand SMILES: c1cc2c(cc1Cl)C(=O)NCC2
Ligand InChI: InChI=1S/C9H8ClNO/c10-7-2-1-6-3-4-11-9(12)8(6)5-7/h1-2,5H,3-4H2,(H,11,12)
Release date: 2015-03-25
Discovery of a novel secreted phospholipase A2 (sPLA2) inhibitor. (PDB entry 5G3M)
Macromolecule: GROUP 10 SECRETORY PHOSPHOLIPASE A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.4
Sequence length: 123 residues
Sequence: GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKCD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1985
R free: 0.23222
Average B factor: 20.746
Crystal growth procedure: 40% PEG 400, 0.1 M BIS-TRIS PH 6.0
Matthews coefficient: 2.22
Solvent content (%): 44.63
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2016-09-14
Crystal structure of ASK1 kinase domain with a potent inhibitor (analog 13) (PDB entry 5VIO)
Macromolecule: Mitogen-activated protein kinase kinase kinase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 293 residues
Sequence: RSTEEGDCESDLLEYDYEYDENGDRVVLGKGTYGIVYAGRDLSNQVRIAIKEIPERDSRYSQPLHEEIALHKHLKHKNIVQYLGSFSENGFIKIFMEQVPGGSLSALLRSKWGPLKDNEQTIGFYTKQILEGLKYLHDNQIVHRDIKGDNVLINTYSGVLKISDFGTSKRLAGINPCTETFTGTLQYMAPEIIDKGPRGYGKAADIWSLGCTIIEMATGKPPFYELGEPQAAMFKVGMFKVHPEIPESMSAEAKAFILKCFEPDPDKRACANDLLVDEFLKVSSKKKKTQPKL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.84
R work: 0.179
R free: 0.216
Average B factor: 109.84
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 0.2M ammonium chloride, 0.1M Bis-Tris (pH 6.1-6.6), and 10% glycerol.
Matthews coefficient: 2.75
Solvent content (%): 55.23
Ligand: 4-methoxy-N~1~-methyl-N~3~-{6-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]pyridin-2-yl}benzene-1,3-dicarboxamide (9E4)
Ligand formula: C20 H22 N6 O3
Ligand molecular weight: 394.427
Ligand SMILES: CC(C)n1cnnc1c2cccc(n2)NC(=O)c3cc(ccc3OC)C(=O)NC
Ligand InChI: InChI=1S/C20H22N6O3/c1-12(2)26-11-22-25-18(26)15-6-5-7-17(23-15)24-20(28)14-10-13(19(27)21-3)8-9-16(14)29-4/h5-12H,1-4H3,(H,21,27)(H,23,24,28)
Release date: 2018-01-17
histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122 (PDB entry 6ACE)
Macromolecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 267 residues
Sequence: PSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.20269
R free: 0.26634
Average B factor: 30.467
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1M sodium cacodylate (pH 5.5), 25%(w/v) PEG 4000
Matthews coefficient: 2.35
Solvent content (%): 47.61
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2019-07-24
Crystal structure of the CK2a/benzoic acid derivative complex (PDB entry 5B0X)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 340 residues
Sequence: GPLGSMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.218
R free: 0.234
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: ethylene glycol
Matthews coefficient: 1.97
Solvent content (%): 37.69
Ligand: 4-[2-[(4-methoxyphenyl)carbonylamino]-1,3-thiazol-5-yl]benzoic acid (HCK)
Ligand formula: C18 H14 N2 O4 S
Ligand molecular weight: 354.38
Ligand SMILES: COc1ccc(cc1)C(=O)Nc2ncc(s2)c3ccc(cc3)C(=O)O
Ligand InChI: InChI=1S/C18H14N2O4S/c1-24-14-8-6-12(7-9-14)16(21)20-18-19-10-15(25-18)11-2-4-13(5-3-11)17(22)23/h2-10H,1H3,(H,22,23)(H,19,20,21)
Release date: 2016-03-30
Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B(S1303D) (PDB entry 7KL0)
Macromolecule: Calcium/calmodulin-dependent protein kinase type II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 268 residues
Sequence: TRFTEEYQLFEELGKGAFSVVRRCVKVLAGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGHHYLIFDLVTGGELFEDIVAREYYSEADASHCIQQILEAVLHCHQMGVVHRNLKPENLLLASKLKGAAVKLADFGLAIEVEGEQQAWFGFAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYKQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPSKRITAAEALKHPWISHR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2071
R free: 0.2584
Average B factor: 23.803
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M 1,3-bis(tris(hydroxymethyl)methylamino)propane, 0.1 M Ammonium sulfate, 20% PEG 6000, 19mM HECAMEG
Matthews coefficient: 2.3
Solvent content (%): 46.54
Ligand: methyl 6-O-(heptylcarbamoyl)-beta-L-altropyranoside (UZD)
Ligand formula: C15 H29 N O7
Ligand molecular weight: 335.393
Ligand SMILES: CCCCCCCNC(=O)OCC1C(C(C(C(O1)OC)O)O)O
Ligand InChI: InChI=1S/C15H29NO7/c1-3-4-5-6-7-8-16-15(20)22-9-10-11(17)12(18)13(19)14(21-2)23-10/h10-14,17-19H,3-9H2,1-2H3,(H,16,20)/t10-,11-,12-,13+,14-/m0/s1
Release date: 2020-12-23
Potempin A (PotA) from Tannerella forsythia in complex with the catalytic domain of human MMP-12 (PDB entry 8B2N)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 158 residues
Sequence: GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.19
R free: 0.228
Average B factor: 40.97
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: The PotA:MMP-12 complex at 8.5 mg/mL in 2.5 mM calcium chloride, 150 mM sodium chloride, 20 mM Tris-HCl pH 7.5 was crystallised from 30% (w/v) PEG 3,000, 200 mM sodium chloride, 100 mM Tris-HCl pH 7.0.
Matthews coefficient: 2.07
Solvent content (%): 40.46
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: 2022-12-21
Crystal structure of human Ephrin type-A receptor 2 (EPHA2) Kinase domain in complex with JG165 (PDB entry 8QQY)
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): 1.8
R work: 0.189
R free: 0.22328
Average B factor: 19.295
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350
10% ethylene glycol
0.2M sodium iodide
Matthews coefficient: 1.97
Solvent content (%): 37.49
Ligand: 6-(4-fluoranyl-3-methoxy-phenyl)-13$l^{6}-thia-2,4,8,12,19-pentazatricyclo[12.3.1.1^{3,7}]nonadeca-1(18),3,5,7(19),14,16-hexaene 13,13-dioxide (WT3)
Ligand formula: C20 H20 F N5 O3 S
Ligand molecular weight: 429.468
Ligand SMILES: COc1cc(ccc1F)c2cnc3nc2NCCCNS(=O)(=O)c4cccc(c4)N3
Ligand InChI: InChI=1S/C20H20FN5O3S/c1-29-18-10-13(6-7-17(18)21)16-12-23-20-25-14-4-2-5-15(11-14)30(27,28)24-9-3-8-22-19(16)26-20/h2,4-7,10-12,24H,3,8-9H2,1H3,(H2,22,23,25,26)
Release date: 2023-11-22
Crystal structure of FGFR4(V550M) kinase domain with 7v (PDB entry 7WCX)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: LLAGLVSLDLPLDPLWEFPRDRLVLGKPLGEGAFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIMECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDEVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.175
R work: 0.1701
R free: 0.2214
Average B factor: 30.627
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris (pH 4.5), 0.2 M Li2SO4, 16-19 % PEG 3350
Matthews coefficient: 2.24
Solvent content (%): 45.18
Ligand: ~{N}-[2-[[5-[(1~{R})-1-[3,5-bis(chloranyl)pyridin-4-yl]ethoxy]-1~{H}-indazol-3-yl]amino]-3-fluoranyl-5-(4-morpholin-4-ylpiperidin-1-yl)phenyl]propanamide (90F)
Ligand formula: C32 H36 Cl2 F N7 O3
Ligand molecular weight: 656.578
Ligand SMILES: CCC(=O)Nc1cc(cc(c1Nc2c3cc(ccc3[nH]n2)OC(C)c4c(cncc4Cl)Cl)F)N5CCC(CC5)N6CCOCC6
Ligand InChI: InChI=1S/C32H36Cl2FN7O3/c1-3-29(43)37-28-15-21(41-8-6-20(7-9-41)42-10-12-44-13-11-42)14-26(35)31(28)38-32-23-16-22(4-5-27(23)39-40-32)45-19(2)30-24(33)17-36-18-25(30)34/h4-5,14-20H,3,6-13H2,1-2H3,(H,37,43)(H2,38,39,40)/t19-/m1/s1
Release date: 2022-03-30
Fragment of human mitochondrial Alanyl-tRNA Synthetase C-Ala domain (PDB entry 6NLY)
Macromolecule: Alanine--tRNA ligase, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.7
Sequence length: 192 residues
Sequence: AATERLSLGSRDVAEALRLSKDIGRLIEAVETAVMPQWQRRELLATVKMLQRRANTAIRKLQMGQAAKKTQELLERHSKGPLIVDTVSAESLSVLVKVVRQLCEQAPSTSVLLLSPQPMGKVLCACQVAQGAMPTFTAEAWALAVCSHMGGKAWGSRVVAQGTGSTTDLEAALSIAQTYALSQLLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.307
R work: 0.2094
R free: 0.257
Average B factor: 77.1161
Crystallization method: EVAPORATION
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Tris-HCl, 40% PEG200
Matthews coefficient: 2.69
Solvent content (%): 54.26
Release date: 2020-01-15
Structure of phosphoY371 c-CBL in complex with ZAP70-peptide and UbV.pCBL ubiquitin variant (PDB entry 5O76)
Macromolecule: Tyrosine protein kinase ZAP70 peptide
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 12 residues
Sequence: TLNSDGYTPEPA
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.473
R work: 0.218
R free: 0.248
Average B factor: 69.77
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M monosaccharides, 0.1 M Buffer 1 pH 6.5, 50% Precipitant 2, Morpheus screen
Matthews coefficient: 2.22
Solvent content (%): 51.42
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: 2017-11-01
Crystal structure of human WEE2 kinase domain in complex with MK1775 (PDB entry 5VDK)
Macromolecule: Wee1-like protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 297 residues
Sequence: GPEFGSTNMASRYEKEFLEVEKIGVGEFGTVYKCIKRLDGCVYAIKRSMKTFTELSNENSALHEVYAHAVLGHHPHVVRYYSSWAEDDHMIIQNEYCNGGSLQAAISENTKSGNHFEEPKLKDILLQISLGLNYIHNSSMVHLDIKPSNIFICHKMQSESSGVIEEVENEADWFLSANVMYKIGDLGHATSINKPKVEEGDSRFLANEILQEDYRHLPKADIFALGLTIAVAAGAESLPTNGAAWHHIRKGNFPDVPQELSESFSSLLKNMIQPDAEQRPSAAALARNTVLRPSLGK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2253
R free: 0.2843
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 14 MG/ML WEE2, 25 mM TRIS PH 8.0, 1 mM DTT, 0.2 M ammonium phosphate monobasic, 1.5 mM MK1775
Matthews coefficient: 2.4
Solvent content (%): 48.72
Ligand: 1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one (8X7)
Ligand formula: C27 H32 N8 O2
Ligand molecular weight: 500.595
Ligand SMILES: CC(C)(c1cccc(n1)N2c3c(cnc(n3)Nc4ccc(cc4)N5CCN(CC5)C)C(=O)N2CC=C)O
Ligand InChI: InChI=1S/C27H32N8O2/c1-5-13-34-25(36)21-18-28-26(29-19-9-11-20(12-10-19)33-16-14-32(4)15-17-33)31-24(21)35(34)23-8-6-7-22(30-23)27(2,3)37/h5-12,18,37H,1,13-17H2,2-4H3,(H,28,29,31)
Release date: 2017-08-23
Crystal Structure of human phosphodiesterase 10 in complex with 1-[2-(3,5-dimethylpyrazol-1-yl)ethyl]-3-(2-phenylpyrazol-3-yl)urea (PDB entry 5SJD)
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): 2.16
R work: 0.1847
R free: 0.2274
Average B factor: 39.981
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: 2.65
Solvent content (%): 53.65
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: 2022-10-12
Crystal structure of DHX8 helicase domain bound to ADP at 2.6 angstrom (PDB entry 6HYS)
Macromolecule: ATP-dependent RNA helicase DHX8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 673 residues
Sequence: ASYGKKTQMSILEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYTKEPETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERMKSLGPDVPELIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNVPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPKDKQALADQKKAKFHQTEGDHLTLLAVYNSWKNNKFSNPWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVSCGKSTVRVQKAICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAPAFFKVSDPTKLSKQKKQQRLEPLYNRYEEPNAWRISRAFRRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.182
R free: 0.214
Average B factor: 67.41
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 15% 2-Methyl-2,4-pentanediol, 100mM Sodium Acetate, 6% DMSO
Matthews coefficient: 2.51
Solvent content (%): 50.92
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2019-08-28