satarupa22/MacromolecularLigandDB huggingface dataset:
EGFR (L858R, T790M, V948R) in complex with 1-[(3R,4R)-3-[({2-[(1-methyl-1H-pyrazol-4-yl)amino]-7H-pyrrolo[2,3-d]pyrimidin-4-yl}oxy)methyl]-4-(trifluoromethyl)pyrrolidin-1-yl]prop-2-en-1-one (PDB entry 5HG9)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 329 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.188
R free: 0.241
Average B factor: 29.9
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 286
Crystal growth procedure: 0.2 M (2.5 uL of stock 4.0 M) Ammonium sulfate, 20.0 %w/v (20.0 uL of stock 50.0 %w/v) PEG 8000, 0.1 M (5.0 uL of stock 1.0 M) HEPES (pH 7.50), 10.4545454545 %v/v (5.2272727272 uL of stock 100.0 %v/v) iso-propanol
Matthews coefficient: 1.86
Solvent content (%): 33.81
Ligand: 1-[(3R,4R)-3-[({2-[(1-methyl-1H-pyrazol-4-yl)amino]-7H-pyrrolo[2,3-d]pyrimidin-4-yl}oxy)methyl]-4-(trifluoromethyl)pyrr
olidin-1-yl]propan-1-one (63A)
Ligand formula: C19 H22 F3 N7 O2
Ligand molecular weight: 437.419
Ligand SMILES: CCC(=O)N1CC(C(C1)C(F)(F)F)COc2c3cc[nH]c3nc(n2)Nc4cnn(c4)C
Ligand InChI: InChI=1S/C19H22F3N7O2/c1-3-15(30)29-7-11(14(9-29)19(20,21)22)10-31-17-13-4-5-23-16(13)26-18(27-17)25-12-6-24-28(2)8-12/h4-6,8,11,14H,3,7,9-10H2,1-2H3,(H2,23,25,26,27)/t11-,14+/m1/s1
Release date: 2016-02-03
Human DDAH1 soaked with its inhibitor ClPyrAA (PDB entry 7ULU)
Macromolecule: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.3.18
Sequence length: 308 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASMAGLGHPAAFGRATHAVVRALPESLGQHALRSAKGEEVDVARAERQHQLYVGVLGSKLGLQVVELPADESLPDCVFVEDVAVVCEETALITRPGAPSRRKEVDMMKEALEKLQLNIVEMKDENATLDGGDVLFTGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVADGLHLKSFCSMAGPNLIAIGSSESAQKALKIMQQMSDHRYDKLTVPDDIAANCIYLNIPNKGHVLLHRTPEEYPESAKVYEKLKDHMLIPVSMSELEKVDGLLTCCSVLINKKVDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2075
R free: 0.2668
Average B factor: 71.5289
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Purified DDAH1 was concentrated to approximately 10 mg/mL using an Amicon-Ultra centrifugal filter device (10 kDa MWCO). The protein was crystallized at 25 C using the hanging drop method (Hampton Research, Aliso Viejo, CA) from 25 % (w/v) PEG6000, 0.1 M Tris-HCl, pH 8.2. Further optimization was done manually using a 1:1 well solution: DDAH1 stock solution ratio to improve crystal size and morphology.  Crystals grew to their maximum size in 3 weeks and were harvested after approximately 25 days. To determine the structure of DDAH1 in complex with ligand, the crystals were transferred to a reservoir containing 20 uL of 20 mM of ligand in the crystallization mother liquor (25% PEG 6000, 0.1 M Tris-HCl, pH 8.2) and soaked for 30 min. Before data collection, crystals with good size and morphology were transferred into a cryoprotection solution (Well Solution supplemented with 25 % (v/v) glycerol) for 1 to 5 seconds using a the cryoloop (Hampton Research, Laguna Niguel, CA). Individual hDDAH1:ligand crystals were flash frozen in liquid nitrogen before use.
Matthews coefficient: 1.95
Solvent content (%): 36.91
Ligand: (2S)-2-amino-4-[(pyridin-2-yl)amino]butanoic acid (NOU)
Ligand formula: C9 H13 N3 O2
Ligand molecular weight: 195.218
Ligand SMILES: c1ccnc(c1)NCCC(C(=O)O)N
Ligand InChI: InChI=1S/C9H13N3O2/c10-7(9(13)14)4-6-12-8-3-1-2-5-11-8/h1-3,5,7H,4,6,10H2,(H,11,12)(H,13,14)/t7-/m0/s1
Release date: 2023-08-30
BTK1 SOAKED WITH COMPOUND 5, Y551 IS SEQUESTERED (PDB entry 7KXM)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 271 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.33
R work: 0.2008
R free: 0.247
Average B factor: 24.45
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 3350
0.1 M Bis Tris Propane pH 7.5
0.2 M Sodium acetate trihydrate
Matthews coefficient: 2.29
Solvent content (%): 46.21
Ligand: 4-tert-butyl-N-(2-methyl-3-{2-[4-(morpholine-4-carbonyl)phenyl]-1H-imidazo[4,5-b]pyridin-7-yl}phenyl)benzamide (X9M)
Ligand formula: C35 H35 N5 O3
Ligand molecular weight: 573.684
Ligand SMILES: Cc1c(cccc1NC(=O)c2ccc(cc2)C(C)(C)C)c3ccnc4c3[nH]c(n4)c5ccc(cc5)C(=O)N6CCOCC6
Ligand InChI: InChI=1S/C35H35N5O3/c1-22-27(6-5-7-29(22)37-33(41)24-12-14-26(15-13-24)35(2,3)4)28-16-17-36-32-30(28)38-31(39-32)23-8-10-25(11-9-23)34(42)40-18-20-43-21-19-40/h5-17H,18-21H2,1-4H3,(H,37,41)(H,36,38,39)
Release date: 2021-05-19
Factor inhibiting HIF-1 alpha in complex with consensus ankyrin repeat domain-(d)allyl-GLY peptide (PDB entry 4NR1)
Macromolecule: Hypoxia-inducible factor 1-alpha inhibitor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.30
Sequence length: 352 residues
Sequence: GSHMAATAAEAVASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.1639
R free: 0.2096
Average B factor: 63.4135
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.6M AMMONIUM SULPHATE, 6% PEG 400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Matthews coefficient: 3.24
Solvent content (%): 62.01
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: 2015-01-21
Factor VIIa in complex with the inhibitor 2-(2-{(R)-[(4-carbamimidoylphenyl)amino][5-ethoxy-2-fluoro-3-(propan-2-yloxy)phenyl]methyl}-1H-imidazol-4-yl)benzamide (PDB entry 4YT7)
Macromolecule: Coagulation factor VII (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): 2.3
R work: 0.1731
R free: 0.1975
Average B factor: 29.71
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES, pH 6.0, 20 mM calcium chloride, 17.5% w/v PEG6000
Matthews coefficient: 3.53
Solvent content (%): 65.13
Ligand: 2-[2-[(R)-[(4-carbamimidoylphenyl)amino]-(5-ethoxy-2-fluoranyl-3-propan-2-yloxy-phenyl)methyl]-1H-imidazol-4-yl]benzamide (4K1)
Ligand formula: C29 H31 F N6 O3
Ligand molecular weight: 530.593
Ligand SMILES: CCOc1cc(c(c(c1)OC(C)C)F)C(c2[nH]cc(n2)c3ccccc3C(=O)N)Nc4ccc(cc4)C(=N)N
Ligand InChI: InChI=1S/C29H31FN6O3/c1-4-38-19-13-22(25(30)24(14-19)39-16(2)3)26(35-18-11-9-17(10-12-18)27(31)32)29-34-15-23(36-29)20-7-5-6-8-21(20)28(33)37/h5-16,26,35H,4H2,1-3H3,(H3,31,32)(H2,33,37)(H,34,36)/t26-/m1/s1
Release date: 2015-04-29
Thiophenyl-Pyrazolourea Derivatives as Potent, Brian Penetrant, Orally Bioavailable, and Isoform-Selective JNK3 Inhibitors (PDB entry 7KSJ)
Macromolecule: Mitogen-activated protein kinase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 464 residues
Sequence: MSLHFLYYCSEPTLDVKIAFCQGFDKQVDVSYIAKHYNMSKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNSEEKTKNGVVKGQPSPSGAAVNSSESLPPSSSVNDISSMSTDQTLASDTDSSLEASAGPLGCCR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.23
R free: 0.2917
Average B factor: 56.77
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.2 M ammonium tartrate pH 7.0, 20 % PEG 3350
Matthews coefficient: 1.88
Solvent content (%): 34.44
Ligand: 4-(4-{[(2-chloro-6-fluorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-N-(oxetan-3-yl)thiophene-2-carboxamide (X3Y)
Ligand formula: C18 H15 Cl F N5 O3 S
Ligand molecular weight: 435.86
Ligand SMILES: c1cc(c(c(c1)Cl)NC(=O)Nc2cnn(c2)c3cc(sc3)C(=O)NC4COC4)F
Ligand InChI: InChI=1S/C18H15ClFN5O3S/c19-13-2-1-3-14(20)16(13)24-18(27)23-10-5-21-25(6-10)12-4-15(29-9-12)17(26)22-11-7-28-8-11/h1-6,9,11H,7-8H2,(H,22,26)(H2,23,24,27)
Release date: 2021-03-03
CBP in complex with Cpd637 ((R)-4-methyl-6-(1-methyl-3-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-5-yl)-1,3,4,5-tetrahydro-2H-benzo[b][1,4]diazepin-2-one) (PDB entry 5I8G)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 264 residues
Sequence: MHHHHHHGSLVPRGSMDYKDDDDKENLYFQGSRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLGYCCGRKYEFSPQTLCCYGKQLCTIPRDAAYYSYQNRYHFCEKCFTEIQGENVTLGDDPSQPQTTISKDQFEKKKNDTLDPEPFVDCKECGRKMHQICVLHYDIIWPSGFVCDNCL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.1888
R free: 0.2105
Average B factor: 34.3308
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: containing 0.1 M Bis-Tris pH 8, 
0.2 M sodium thiocyanate 
19-23% PEG 3350
Matthews coefficient: 2.34
Solvent content (%): 47.41
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: 2016-04-20
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z319545618 (PDB entry 5RXT)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1878
R free: 0.2176
Average B factor: 19.922
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.11
Solvent content (%): 41.64
Ligand: 3-[(2-methyl-1H-imidazol-1-yl)methyl]benzonitrile (RXS)
Ligand formula: C12 H11 N3
Ligand molecular weight: 197.236
Ligand SMILES: Cc1nccn1Cc2cccc(c2)C#N
Ligand InChI: InChI=1S/C12H11N3/c1-10-14-5-6-15(10)9-12-4-2-3-11(7-12)8-13/h2-7H,9H2,1H3
Release date: 2020-11-11
Crystal structure of the WWP2 HECT domain in complex with H304, a Helicon Polypeptide (PDB entry 8EI7)
Macromolecule: NEDD4-like E3 ubiquitin-protein ligase WWP2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 376 residues
Sequence: GPDRSFRWKYHQFRFLCHSNALPSHVKISVSRQTLFEDSFQQIMNMKPYDLRRRLYIIMRGEEGLDYGGIAREWFFLLSHEVLNPMYCLFEYAGKNNYCLQINPASSINPDHLTYFRFIGRFIAMALYHGKFIDTGFTLPFYKRMLNKRPTLKDLESIDPEFYNSIVWIKENNLEECGLELYFIQDMEILGKVTTHELKEGGESIRVTEENKEEYIMLLTDWRFTRGVEEQTKAFLDGFNEVAPLEWLRYFDEKELELMLCGMQEIDMSDWQKSTIYRHYTKNSKQIQWFWQVVKEMDNEKRIRLLQFVTGTCRLPVGGFAELIGSNGPQKFCIDKVGKETWLPRSHTCFNRLDLPPYKSYEQLREKLLYAIEETE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.1999
R free: 0.2638
Average B factor: 47.9493
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.2M magnesium chloride, 0.1M Bis-tris pH7.5, 30% PEG3350
Matthews coefficient: 2.25
Solvent content (%): 45.41
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: 2023-10-25
Crystal Structure of Mek1(NQ)NES peptide bound to CRM (PDB entry 6X2S)
Macromolecule: GTP-binding nuclear protein Ran
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 216 residues
Sequence: MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.496
R work: 0.1961
R free: 0.2464
Average B factor: 43.622
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 273
Crystal growth procedure: 17% (weight/vol) PEG3350, 100 mM Bis-Tris (pH 6.4), 200 mM ammonium nitrate, and 10 mM Spermine HCl
Matthews coefficient: 2.71
Solvent content (%): 54.54
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2020-07-01
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMSOA000951b (PDB entry 5QF7)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1819
R free: 0.2107
Average B factor: 39.385
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.31
Solvent content (%): 62.84
Ligand: 1-(3,4-dichlorophenyl)propan-2-one (JNV)
Ligand formula: C9 H8 Cl2 O
Ligand molecular weight: 203.065
Ligand SMILES: CC(=O)Cc1ccc(c(c1)Cl)Cl
Ligand InChI: InChI=1S/C9H8Cl2O/c1-6(12)4-7-2-3-8(10)9(11)5-7/h2-3,5H,4H2,1H3
Release date: 2018-10-10
Human endothelin receptor type-B in complex with inverse agonist IRL2500 (PDB entry 6K1Q)
Macromolecule: Endothelin B receptor,Endolysin,Endothelin B receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 464 residues
Sequence: GGGLAPAEVPKGDRTAGSPPRTISPPPCQGPIEIKETFKYINTVVSCLVFVLGIIGNSTLLYIIYKNKCMRNGPNILIASLALGDLLHIVIDIPINVYKLLAEDWPFGAEMCKLVPFIQKASVGITVLSLCALSIDRYRAVASWSRIKGIGVPKWTAVEIVLIWVVSVVLAVPEAIGFDIITMDYKGSYLRICLLHPVQKTAFMQFYATAKDWWLFSFYFCLPLAITAFFYTLMTCEMLRKNIFEMLRIDEGGGSGGDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYLNDHLKQRREVAKTVFCLVLVFALCWLPLHLARILKLTLYNQNDPNRCELLSFLLVLDYIGINMASLNSCANPIALYLVSKRFKNAFKSALCCWAQSPSSENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2216
R free: 0.2653
Average B factor: 83.7693
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG300, 150 mM NaH2PO4,10 mM TCEP, 100 mM Bis-tris
Matthews coefficient: 4.22
Solvent content (%): 70.88
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: 2019-07-17
Selective inhibition of carbonic anhydrase IX activity, using compound SLC-149, displays limited anticancer effects in breast cancer cell lines (PDB entry 6NLV)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.794
R work: 0.2167
R free: 0.2554
Average B factor: 20.4085
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6 M Sodium citrate, 50 mM Tris HCl, pH 7.8
Matthews coefficient: 2.07
Solvent content (%): 40.49
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: 2020-01-15
Thrombin in complex with D-Phe-Pro-2-chlorothiophen derivative (16e) (PDB entry 6YHJ)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.1274
R free: 0.1541
Average B factor: 23.489
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20mM sodium dihydrogen phosphate ph 7.5
350mM NaCl
27% PEG 8000
Matthews coefficient: 2.42
Solvent content (%): 49.14
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2021-04-14
Structure of human TUT7 catalytic module (CM) in complex with U5 RNA (PDB entry 5W0M)
Macromolecule: Terminal uridylyltransferase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.52
Sequence length: 389 residues
Sequence: GAGAGSKRIQLEPLPPLTPKFLNILDQVCIQCYKDFSPTIIEDQAREHIRQNLESFIRQDFPGTKLSLFGSSKNGFGFKQSDLAVCMTINGLETAEGLDCVRTIEELARVLRKHSGLRNILPITTAKVPIVKFFHLRSGLEVDISLYNTLALHNTRLLSAYSAIDPRVKYLCYTMKVFTKMCDIGDASRGSLSSYAYTLMVLYFLQQRNPPVIPVLQEIYKGEKKPEIFVDGWNIYFFDQIDELPTYWSECGKNTESVGQLWLGLLRFYTEEFDFKEHVISIRRKSLLTTFKKQWTSKYIVIEDPFDLNHNLGAGLSRKMTNFIMKAFINGRRVFGIPVKGFPKDYPSKMEYFFDPDVLTEGELAPNDRCCRICGKIGHFMKDCPMRRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.298
R work: 0.1883
R free: 0.2287
Average B factor: 65.9348
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.8-1.0 M lithium sulfate, 0.075-0.2 M potassium iodide, 0.05-0.2 M trisodium citrate, pH 5-6
Matthews coefficient: 3.42
Solvent content (%): 64.06
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: 2017-06-28
HDM2 in complex with a 3,3-Disubstituted Piperidine (PDB entry 5HMI)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 104 residues
Sequence: QIQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLYYLGQYIMTKRLYDEKQQHIVHCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSAGA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.2076
R free: 0.2289
Average B factor: 52.9
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.2
Crystallization temperature (K): 303
Crystal growth procedure: 1.8-2.2 M ammonium sulfate, 100 mM NaCitrate/Citric acid
Matthews coefficient: 2.21
Solvent content (%): 44.39
Ligand: {4-[2-(2-hydroxyethoxy)phenyl]piperazin-1-yl}[(2R,3S)-2-propyl-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}-3-{[5-(trifluoromethyl)thiophen-3-yl]oxy}piperidin-3-yl]methanone (62T)
Ligand formula: C33 H36 F6 N4 O5 S
Ligand molecular weight: 714.718
Ligand SMILES: CCCC1C(CCCN1C(=O)c2cnccc2C(F)(F)F)(C(=O)N3CCN(CC3)c4ccccc4OCCO)Oc5cc(sc5)C(F)(F)F
Ligand InChI: InChI=1S/C33H36F6N4O5S/c1-2-6-27-31(48-22-19-28(49-21-22)33(37,38)39,10-5-12-43(27)29(45)23-20-40-11-9-24(23)32(34,35)36)30(46)42-15-13-41(14-16-42)25-7-3-4-8-26(25)47-18-17-44/h3-4,7-9,11,19-21,27,44H,2,5-6,10,12-18H2,1H3/t27-,31+/m1/s1
Release date: 2016-04-06
Crystal structure of PDE10A in complex with a triazolopyrimidine inhibitor (PDB entry 6KDX)
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: 345 residues
Sequence: GSHMSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.44
R work: 0.2414
R free: 0.3009
Average B factor: 56.869
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 50mM Bis-tris propane pH6.0, 50mM Magnesium sulfate, 15% PEG 3350
Matthews coefficient: 2.19
Solvent content (%): 43.73
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2019-08-14