satarupa22/MacromolecularLigandDB huggingface dataset:
Pi3K alpha lipid kinase with Active Site Inhibitor (PDB entry 4YKN)
Macromolecule: Phosphatidylinositol 3-kinase regulatory subunit alpha,Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform fusion protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 1383 residues
Sequence: MHHHHHHANNGMNNNMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKKLNEWLGNENTEDQYSLVEDDEDGSPGISGGGGGPPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTTKMDWIFHTIKQHALN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2015
R free: 0.2472
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: ethylenene glycol, PIP2
Matthews coefficient: 2.94
Solvent content (%): 58.18
Ligand: 3-(6-methoxypyridin-3-yl)-5-[({4-[(5-methyl-1,3,4-thiadiazol-2-yl)sulfamoyl]phenyl}amino)methyl]benzoic acid (4EL)
Ligand formula: C23 H21 N5 O5 S2
Ligand molecular weight: 511.573
Ligand SMILES: Cc1nnc(s1)NS(=O)(=O)c2ccc(cc2)NCc3cc(cc(c3)C(=O)O)c4ccc(nc4)OC
Ligand InChI: InChI=1S/C23H21N5O5S2/c1-14-26-27-23(34-14)28-35(31,32)20-6-4-19(5-7-20)24-12-15-9-17(11-18(10-15)22(29)30)16-3-8-21(33-2)25-13-16/h3-11,13,24H,12H2,1-2H3,(H,27,28)(H,29,30)
Release date: 2015-06-17
Crystal Structure of the CBP in complex with the Y08188 (PDB entry 7XM7)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 133 residues
Sequence: MKKGHHHHHHLVPRGSRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.36
R work: 0.208
R free: 0.2566
Average B factor: 39.523
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG3350 0.2M NH4NO3 PH6.2
Matthews coefficient: 2.11
Solvent content (%): 41.58
Ligand: 3-ethanoyl-~{N}-[2-fluoranyl-3-(1-methylpyrazol-4-yl)phenyl]-7-methoxy-indolizine-1-carboxamide (GAY)
Ligand formula: C22 H19 F N4 O3
Ligand molecular weight: 406.41
Ligand SMILES: CC(=O)c1cc(c2n1ccc(c2)OC)C(=O)Nc3cccc(c3F)c4cnn(c4)C
Ligand InChI: InChI=1S/C22H19FN4O3/c1-13(28)19-10-17(20-9-15(30-3)7-8-27(19)20)22(29)25-18-6-4-5-16(21(18)23)14-11-24-26(2)12-14/h4-12H,1-3H3,(H,25,29)
Release date: 2022-06-22
Crystal structure of CHK1-10pt-mutant complex with compound 13 (PDB entry 7BJO)
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): 2.3
R work: 0.1625
R free: 0.2074
Average B factor: 39.804
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol
Matthews coefficient: 2.34
Solvent content (%): 47.51
Ligand: 4-amino-6-(2,3-difluorophenyl)-7-methyl-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile (TWK)
Ligand formula: C14 H9 F2 N5
Ligand molecular weight: 285.252
Ligand SMILES: Cn1c(c(c2c1ncnc2N)C#N)c3cccc(c3F)F
Ligand InChI: InChI=1S/C14H9F2N5/c1-21-12(7-3-2-4-9(15)11(7)16)8(5-17)10-13(18)19-6-20-14(10)21/h2-4,6H,1H3,(H2,18,19,20)
Release date: 2021-07-07
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with NVP-BHG712 (PDB entry 6FNF)
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): 1.556
R work: 0.2351
R free: 0.2727
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 37.5 % MPD/PEG1000/PEG3350 (MD), 0.1 M Amino Acids Mix (MD), 0.1 M Tris pH 7.5
Matthews coefficient: 1.86
Solvent content (%): 33.83
Ligand: 4-methyl-3-[(1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]-~{N}-[3-(trifluoromethyl)phenyl]benzamide (DXH)
Ligand formula: C26 H20 F3 N7 O
Ligand molecular weight: 503.479
Ligand SMILES: Cc1ccc(cc1Nc2c3cnn(c3nc(n2)c4cccnc4)C)C(=O)Nc5cccc(c5)C(F)(F)F
Ligand InChI: InChI=1S/C26H20F3N7O/c1-15-8-9-16(25(37)32-19-7-3-6-18(12-19)26(27,28)29)11-21(15)33-23-20-14-31-36(2)24(20)35-22(34-23)17-5-4-10-30-13-17/h3-14H,1-2H3,(H,32,37)(H,33,34,35)
Release date: 2018-08-08
Structure of Lpg2148/UBE2N-Ub complex (PDB entry 6LP2)
Macromolecule: Ubiquitin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 76 residues
Sequence: MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.479
R work: 0.1751
R free: 0.2326
Average B factor: 39.0475
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: PEG 3350, potassium citrate
Matthews coefficient: 2.68
Solvent content (%): 54.07
Release date: 2021-01-13
Apo X-ray crystal structure of Cyclophilin D with a surface entropy reduction mutation (K175I) (PDB entry 8UC4)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 166 residues
Sequence: SNANPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.1822
R free: 0.2109
Average B factor: 25.14
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: Well solution: 40% w/v PEG3350, 30 mM NaCl, 50 mM potassium phosphate monobasic pH 7.0
Protein Solution: 15 mg/mL protein, 20 mM Tris pH 8.0, 50 mM NaCl, 1 mM DTT, and 5% glycerol
Drop: 1 uL protein solution, 1 uL well solution
Matthews coefficient: 2.49
Solvent content (%): 50.64
Ligand: POLYETHYLENE GLYCOL (N=34) (15P)
Ligand formula: C69 H140 O35
Ligand molecular weight: 1529.829
Ligand SMILES: COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
Ligand InChI: InChI=1S/C69H140O35/c1-71-4-5-73-8-9-75-12-13-77-16-17-79-20-21-81-24-25-83-28-29-85-32-33-87-36-37-89-40-41-91-44-45-93-48-49-95-52-53-97-56-57-99-60-61-101-64-65-103-68-69-104-67-66-102-63-62-100-59-58-98-55-54-96-51-50-94-47-46-92-43-42-90-39-38-88-35-34-86-31-30-84-27-26-82-23-22-80-19-18-78-15-14-76-11-10-74-7-6-72-3-2-70/h70H,2-69H2,1H3
Release date: 2024-08-07
Human STK10 (LOK) with SB-633825 (PDB entry 4USE)
Macromolecule: SERINE/THREONINE-PROTEIN KINASE 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 302 residues
Sequence: SMRKSREYEHVRRDLDPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIETKSEEELEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVLMTLEGDIRLADFGVSAKNLKTLQKRDSFIGTPYWMAPEVVMCETMKDTPYDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDPPTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAEVMEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.22454
R free: 0.25145
Average B factor: 72.105
Crystallization pH: 6.5
Crystal growth procedure: 50% (V/V) PEG 300, 0.1M CACODYLATE PH 6.5, 0.2M MGCL2
Matthews coefficient: 3
Solvent content (%): 59
Ligand: 4-{5-(6-methoxynaphthalen-2-yl)-1-methyl-2-[2-methyl-4-(methylsulfonyl)phenyl]-1H-imidazol-4-yl}pyridine (R09)
Ligand formula: C28 H25 N3 O3 S
Ligand molecular weight: 483.581
Ligand SMILES: Cc1cc(ccc1c2nc(c(n2C)c3ccc4cc(ccc4c3)OC)c5ccncc5)S(=O)(=O)C
Ligand InChI: InChI=1S/C28H25N3O3S/c1-18-15-24(35(4,32)33)9-10-25(18)28-30-26(19-11-13-29-14-12-19)27(31(28)2)22-6-5-21-17-23(34-3)8-7-20(21)16-22/h5-17H,1-4H3
Release date: 2015-07-22
Crystal Structure of human phosphodiesterase 10 in complex with N-(3-imidazo[1,2-a]pyridin-2-ylphenyl)-1-methyl-3-(pyrimidin-5-ylamino)pyrazole-4-carboxamide (PDB entry 5SKO)
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): 2.1
R work: 0.1935
R free: 0.2309
Average B factor: 41.127
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: 3.05
Solvent content (%): 59.61
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
Human carbonic anhydrase II (F131Y) complexed with benzo[d]thiazole-2-sulfonamide (PDB entry 5JE7)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDYGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.15
R work: 0.1215
R free: 0.1435
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: We soaked monoclinic crystals of HCAII with BTA by carrying out the following steps: (i) We prepared soaking solutions containing 1.32 M sodium citrate, 1 mM ZnSO4, 100 mM Tris-HCl (pH 7.8), and 5 mM ligand. (ii) We combined 4 uL of soaking solution and 1-2 crystals of HCAII within a drop on the surface of a reservoir cover (EasyXtal CrystalSupport, Qiagen). (iii) To a clear plastic reservoir in a 15-reservoir plate (EasyXtal, Qiagen), we added 1 mL of soaking solution (without ligand present). We attached the reservoir cover to the reservoir and left the entire setup at 4 deg C for 1 week.
Matthews coefficient: 2.12
Solvent content (%): 41.85
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: 2017-01-11
Human heparanase in complex with inhibitor R3794 (PDB entry 8CQI)
Macromolecule: Heparanase 50 kDa subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 389 residues
Sequence: DPGKKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.19878
R free: 0.25256
Average B factor: 41.776
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 5.5, 0.1M magnesium chloride, 18% PEG 3,350
Matthews coefficient: 2.53
Solvent content (%): 51.32
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2024-01-10
Crystal structure of TNKS2 in complex with 2-(4-methylpiperazin-1-yl)- 3,4,5,6,7,8-hexahydroquinazolin-4-one (PDB entry 5AL4)
Macromolecule: TANKYRASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 240 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.167
R free: 0.19779
Average B factor: 27.65
Crystallization pH: 8.5
Crystal growth procedure: pH 8.5
Matthews coefficient: 2.4
Solvent content (%): 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: 2015-07-29
Crystal structure of human DDR1 in complex with CH5541127 (PDB entry 7FEH)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 320 residues
Sequence: GPLHMPGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.61
R work: 0.1655
R free: 0.2057
Average B factor: 24.9512
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.6
Crystallization temperature (K): 285
Crystal growth procedure: 10 mg/mL protein, 1 mM Ligand, 2 %(v/v) DMSO, 21.0 %(w/v) PEG 2000 MME, 0.25 M NaNO3, 0.1 M BIS-TRIS propane (pH 6.6), 5.0 %(v/v) PEG 400
Matthews coefficient: 2.09
Solvent content (%): 41.01
Ligand: N-[(5-chloranyl-2-ethylsulfonyl-phenyl)methyl]-3-piperazin-1-yl-5-(trifluoromethyloxy)benzamide (3UI)
Ligand formula: C21 H23 Cl F3 N3 O4 S
Ligand molecular weight: 505.938
Ligand SMILES: CCS(=O)(=O)c1ccc(cc1CNC(=O)c2cc(cc(c2)OC(F)(F)F)N3CCNCC3)Cl
Ligand InChI: InChI=1S/C21H23ClF3N3O4S/c1-2-33(30,31)19-4-3-16(22)9-15(19)13-27-20(29)14-10-17(28-7-5-26-6-8-28)12-18(11-14)32-21(23,24)25/h3-4,9-12,26H,2,5-8,13H2,1H3,(H,27,29)
Release date: 2022-07-27
Human DNA Pol eta with dA-ended primer and dATP: in crystallo reaction for 0 s (PDB entry 7M7Y)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1763
R free: 0.2214
Average B factor: 26.2063
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: 15% PEG 2000 MME,
100 mM MES
Matthews coefficient: 2.13
Solvent content (%): 42.15
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: 2021-06-02
Crystal structure of human AKR1B10 complexed with NADP+ and the inhibitor MK181 (PDB entry 5LIK)
Macromolecule: Aldo-keto reductase family 1 member B10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 316 residues
Sequence: MATFVELSTKAKMPIVGLGTWKSPLGKVKEAVKVAIDAGYRHIDCAYVYQNEHEVGEAIQEKIQEKAVKREDLFIVSKLWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIHWPQGFKSGDDLFPRDDKGNAIGGKATFLDAWEAMEELVDEGLVKALGVSNFSHFQIEKLLNKPGLKYKPVTNQVECHPYLTQEKLIQYCHSKGITVTAYSPLGSPDRPWAKPEDPSLLEDPKIKEIAAKHKKTAAQVLIRFHIQRNVIVIPKSVTPARIVENIQVFDFKLSDEEMATILSFNRNWRACNLLQSSHLEDYPFNAEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2009
R free: 0.2444
Average B factor: 34.63
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG 6000, 100 mM sodium cacodylate
Matthews coefficient: 2.37
Solvent content (%): 48.03
Ligand: {2-[(4-bromobenzyl)carbamoyl]-5-chlorophenoxy}acetic acid (W8X)
Ligand formula: C16 H13 Br Cl N O4
Ligand molecular weight: 398.636
Ligand SMILES: c1cc(ccc1CNC(=O)c2ccc(cc2OCC(=O)O)Cl)Br
Ligand InChI: InChI=1S/C16H13BrClNO4/c17-11-3-1-10(2-4-11)8-19-16(22)13-6-5-12(18)7-14(13)23-9-15(20)21/h1-7H,8-9H2,(H,19,22)(H,20,21)
Release date: 2016-07-27
Crystal structure of human guanylate-binding protein 2 (hGBP2) K51A mutant (PDB entry 7M1S)
Macromolecule: Guanylate-binding protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 591 residues
Sequence: MAPEINLPGPMSLIDNTKGQLVVNPEALKILSAITQPVVVVAIVGLYRTGASYLMNKLAGKKNGFSLGSTVKSHTKGIWMWCVPHPKKPEHTLVLLDTEGLGDIEKGDNENDSWIFALAILLSSTFVYNSMGTINQQAMDQLHYVTELTDRIKANSSPGNNSVDDSADFVSFFPAFVWTLRDFTLELEVDGEPITADDYLELSLKLRKGTDKKSKSFNDPRLCIRKFFPKRKCFVFDWPAPKKYLAHLEQLKEEELNPDFIEQVAEFCSYILSHSNVKTLSGGIPVNGPRLESLVLTYVNAISSGDLPCRENAVLALAQIENSAAVEKAIAHYEQQMGQKVQLPTETLQELLDLHRDSEREAIEVFMKNSFKDVDQMFQRKLGAQLEARRDDFCKQNSKASSDCCMALLQDIFGPLEEDVKQGTFSKPGGYRLFTQKLQELKNKYYQVPRKGIQAKEVLKKYLESKEDVADALLQTDQSLSEKEKAIEVERIKAESAEAAKKMLEEIQKKNEEMMEQKEKSYQEHVKQLTEKMERDRAQLMAEQEKTLALKLQEQERLLKEGFENESKRLQKDIWDIQMRSKSLEPICNIL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.91
R work: 0.2451
R free: 0.2736
Average B factor: 100.5535
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289.15
Crystal growth procedure: 0.7M NaH2PO4, 1.05M K2HPO4, 0.1M sodium acetate pH 3.8
Matthews coefficient: 3.74
Solvent content (%): 67.12
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: 2022-04-27
Factor XIa in Complex with Compound 2j (PDB entry 7V16)
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): 1.505
R work: 0.1658
R free: 0.1942
Average B factor: 30.1471
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 4000, 100mM Na Citrate pH 5.0
Matthews coefficient: 2.21
Solvent content (%): 44.39
Ligand: CITRIC ACID (CIT)
Ligand formula: C6 H8 O7
Ligand molecular weight: 192.124
Ligand SMILES: C(C(=O)O)C(CC(=O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)
Release date: 2022-08-03
Human SIRT2 catalyse short chain fatty acyl lysine (PDB entry 5G4C)
Macromolecule: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 323 residues
Sequence: GEADMDFLRNLFSQTLSLGSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.183
R free: 0.2198
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 291
Crystal growth procedure: 12% PEG 8K, 0.1 M HEPES, PH 7.5, 5% ISOPROPANOL
Matthews coefficient: 2.23
Solvent content (%): 44.88
Ligand: CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE (CNA)
Ligand formula: C22 H30 N7 O13 P2
Ligand molecular weight: 662.46
Ligand SMILES: c1cc(c[n+](c1)C2CC(C(C2O)O)COP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)C(=O)N
Ligand InChI: InChI=1S/C22H29N7O13P2/c23-19-14-21(26-8-25-19)29(9-27-14)22-18(33)17(32)13(41-22)7-40-44(37,38)42-43(35,36)39-6-11-4-12(16(31)15(11)30)28-3-1-2-10(5-28)20(24)34/h1-3,5,8-9,11-13,15-18,22,30-33H,4,6-7H2,(H5-,23,24,25,26,34,35,36,37,38)/p+1/t11-,12-,13-,15-,16+,17-,18-,22-/m1/s1
Release date: 2017-05-03