satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the YFPnano fusion protein (PDB entry 6HR1)
Macromolecule: Myosin light chain kinase 2, skeletal/cardiac muscle,Unconventional myosin-X,Green fluorescent protein,Calmodulin-1
Type: Protein, polypeptide(L)
Source organism: Oryctolagus cuniculus
EC number: 2.7.11.18
Sequence length: 434 residues
Sequence: GPHMARWKKAFIAVSAANRFKKISSEEEKRKREEEEVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFGYGLQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKGENLYFQSGGSAAAADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.901
R work: 0.1806
R free: 0.2136
Average B factor: 36.7914
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 24% w/v PEG 3350
0.2 M di-Ammonium tartrate 
10% v/v Glycerol
Matthews coefficient: 2.67
Solvent content (%): 54.01
Ligand: L(+)-TARTARIC ACID (TLA)
Ligand formula: C4 H6 O6
Ligand molecular weight: 150.087
Ligand SMILES: C(C(C(=O)O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/t1-,2-/m1/s1
Release date: 2020-04-08
Crystal structure of the NTF2L domain of human G3BP1 in complex with the Caprin-1 derived peptide (PDB entry 7XHG)
Macromolecule: Ras GTPase-activating protein-binding protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 139 residues
Sequence: MVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFG
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.46
R work: 0.206
R free: 0.2746
Average B factor: 39.622
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289.15
Crystal growth procedure: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30 % w/v Polyethylene glycol 8,000
Matthews coefficient: 2.34
Solvent content (%): 47.36
Release date: 2023-01-18
ASH1L SET domain K2264L mutant in complex with S-adenosyl methionine (SAM) (PDB entry 4YPU)
Macromolecule: Histone-lysine N-methyltransferase ASH1L
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 226 residues
Sequence: GAMAGSYKKIRSNVYVDVKPLSGYEATTCNCKKPDDDTRKGCVDDCLNRMIFAECSPNTCPCGEQCCNQRIQRHEWVQCLERFRAEEKGWGIRTKEPLKAGQFIIEYLGEVVSEQEFRNRMIEQYHNHSDHYCLNLDSGMVIDSYRMGNEARFINHSCDPNCEMQKWSVNGVYRIGLYALKDMPAGTELTYDYNFHSFNVELQQLCKCGFEKCRGIIGGKSQRVNG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2379
R free: 0.3053
Average B factor: 53.136
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG 3350, 20 mm Tris
Matthews coefficient: 2.19
Solvent content (%): 43.89
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2015-09-02
Crystal structure of MELK in complex with an inhibitor (PDB entry 5MAG)
Macromolecule: Maternal embryonic leucine zipper kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 347 residues
Sequence: GPKDYDELLKYYELHETIGTGGFAKVKLACHILTGEMVAIKIMDKNTLGSDLPRIKTEIEALKNLRHQHICQLYHVLETANKIFMVLEYCPGGELFDYIISQDRLSEEETRVVFRQIVSAVAYVHSQGYAHRDLKPENLLFDEYHKLKLIDFGLCAKPKGNKDYHLQTCCGSLAYAAPELIQGKSYLGSEADVWSMGILLYVLMCGFLPFDDDNVMALYKKIMRGKYDVPKWLSPSSILLLQQMLQVDPKKRISMKNLLNHPWIMQDYNYPVEWQSKNPFIHLDDDCVTELSVHHRNNRQTMEDLISLWQYDHLTATYLLLLAKKARGKPVRLRLSSFSCGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.19351
R free: 0.25242
Average B factor: 36.056
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 10-20% PEG 3350 or PEG 4000, 0.1 M BIS TRIS pH 6.5, 0.6M NaCl
Matthews coefficient: 2.26
Solvent content (%): 45.28
Ligand: PF-3758309 (7KC)
Ligand formula: C25 H30 N8 O S
Ligand molecular weight: 490.624
Ligand SMILES: Cc1nc2ccsc2c(n1)Nc3c4c([nH]n3)C(N(C4)C(=O)NC(CN(C)C)c5ccccc5)(C)C
Ligand InChI: InChI=1S/C25H30N8OS/c1-15-26-18-11-12-35-20(18)23(27-15)29-22-17-13-33(25(2,3)21(17)30-31-22)24(34)28-19(14-32(4)5)16-9-7-6-8-10-16/h6-12,19H,13-14H2,1-5H3,(H,28,34)(H2,26,27,29,30,31)/t19-/m1/s1
Release date: 2017-12-06
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMSOA001247b (PDB entry 5QEJ)
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): 1.924
R work: 0.2012
R free: 0.2422
Average B factor: 45.9098
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: 3.34
Solvent content (%): 63.14
Ligand: 2,6-dichloropyridine-4-carboxylic acid (JKP)
Ligand formula: C6 H3 Cl2 N O2
Ligand molecular weight: 192
Ligand SMILES: c1c(cc(nc1Cl)Cl)C(=O)O
Ligand InChI: InChI=1S/C6H3Cl2NO2/c7-4-1-3(6(10)11)2-5(8)9-4/h1-2H,(H,10,11)
Release date: 2018-10-10
Notum Fragment 784 (PDB entry 7BCI)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.2372
R free: 0.2482
Average B factor: 27.1844
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.98
Solvent content (%): 37.95
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: 2022-01-12
BTK complex with compound 11 (PDB entry 6BKH)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 287 residues
Sequence: MGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDENLYFQGEEYMPTEHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.792
R work: 0.1524
R free: 0.2008
Average B factor: 28.6707
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: PEG 10000, Li2SO4, pH 7.0
Matthews coefficient: 2.09
Solvent content (%): 41.01
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2018-11-07
Crystal structure of MerTK kinase domain in complex with UNC2025 (PDB entry 7AB2)
Macromolecule: Tyrosine-protein kinase Mer
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 298 residues
Sequence: GSHMEELQNKLEDVVIDRNLLILGRILGEGEFGSVMEGNLKQEDGTSLKVAVKTMKLDNSSQREIEEFLSEAACMKDFSHPNVIRLLGVCIEMSSQGIPKPMVILPFMKYGDLHTYLLYSRLETGPRHIPLQTLLRFMVDIALGMEYLSNRNFLHRDLAARNCMLRDDMTVCVADFGLSKKIYSGDYYRQGRIAKMPVKWIAIESLADRVYTSKSDVWAFGVTMWEIATRGMTPYPGVQNHEMYDYLLHGHRLKQPEDCLDELYEIMYSCWRTDPLDRPTFSVLRLQLERLLESLPDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.1933
R free: 0.2497
Average B factor: 48.966
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris pH 8.5, 4.3M NaCl
Matthews coefficient: 2.2
Solvent content (%): 44.12
Ligand: 4-[2-(butylamino)-5-[4-[(4-methylpiperazin-1-yl)methyl]phenyl]pyrrolo[2,3-d]pyrimidin-7-yl]cyclohexan-1-ol (R6N)
Ligand formula: C28 H40 N6 O
Ligand molecular weight: 476.657
Ligand SMILES: CCCCNc1ncc2c(cn(c2n1)C3CCC(CC3)O)c4ccc(cc4)CN5CCN(CC5)C
Ligand InChI: InChI=1S/C28H40N6O/c1-3-4-13-29-28-30-18-25-26(20-34(27(25)31-28)23-9-11-24(35)12-10-23)22-7-5-21(6-8-22)19-33-16-14-32(2)15-17-33/h5-8,18,20,23-24,35H,3-4,9-17,19H2,1-2H3,(H,29,30,31)/t23-,24-
Release date: 2020-10-28
Carbonic anhydrase 2 with inhibitor (2Z)-3-oxo-N-(4-sulfamoylphenyl)-2-[(thiophen-2-yl)methylidene]butanamide (11g/D7) (PDB entry 6UFD)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.48
R work: 0.1494
R free: 0.1674
Average B factor: 13.836
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 200 nL 7 mg/mL protein + 200 nL reservoir solution (2.5-2.8 M ammonium sulfate, 100 mM Tris, pH 8.5-9.0)
Matthews coefficient: 2.12
Solvent content (%): 41.96
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: 2020-08-05
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z4605084898 (PDB entry 7G98)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.878
R work: 0.209
R free: 0.2946
Average B factor: 70.25
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.48
Solvent content (%): 50.42
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2023-07-12
Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with the tricyclic inhibitor (3) (PDB entry 7BLE)
Macromolecule: Nicotinamide N-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.1
Sequence length: 283 residues
Sequence: MGSSHHHHHHSSGLVPRGSMESGFTSKDTYLSHFNPRDYLEKYYKFGSRHSAESQILKHLLKNLFKIFCLDGVKGDLLIDIGSGPTIYQLLSACESFKEIVVTDYSDQNLQELEKWLKAAPAAFDWSPVVTYVCDLEGNRVKGPEKEEKLRQAVKQVLKCDVTQSQPLGAVPLPPADCVLSTLCLDAACPDLPTYCRALRNLGSLLKPGGFLVIMDALKSSYYMIGEQKFSSLPLGREAVEAAVKEAGYTIEWFEVISQSYSSTMANNEGLFSLVARKLSRPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.809
R work: 0.1864
R free: 0.2696
Average B factor: 30.66
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Human NNMT was crystallized using the following conditions: A protein solution with 6 mg/ml NNMT, 50 mM Tris/HCL, pH 8.0, 1 mM DTT, 86uM S-Adenosyl-L-Homocysteine (SAH), 0.95mM inhibitor and 5% v/v glycerol was equilibrated at room temperature in a hanging drop setup against 2.2 M ammonium sulfate with 0.1 M HEPES/Na, pH 7.6. Small crystal appeared after 1-2 weeks.
Matthews coefficient: 2.23
Solvent content (%): 44.89
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2021-03-17
SETD3 in Complex with an Actin Peptide with His73 Replaced with Lysine (PDB entry 6OX3)
Macromolecule: Actin Peptide
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 19 residues
Sequence: TLKYPIEKGIVTNWDDMEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.785
R work: 0.2079
R free: 0.2465
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 292
Crystal growth procedure: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000
Matthews coefficient: 3.03
Solvent content (%): 59.4
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: 2019-08-21
Structure determination of a potent, selective antibody inhibitor of human MMP9 (apo MMP9) (PDB entry 5TH6)
Macromolecule: Matrix metalloproteinase-9,Matrix metalloproteinase-9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.35
Sequence length: 231 residues
Sequence: MATDRQLAEEYLYRYGYTRVAEMRGESKSLGPALLLLQKQLSLPETGELDSATLKAMRTPRCGVPDLGRFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGQGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2075
R free: 0.2346
Average B factor: 16.3579
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 12% (v/v) PEG 8000
0.3 M lithium sulfate
0.1 M sodium acetate, pH 5.0
Matthews coefficient: 2.1
Solvent content (%): 41.44
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: 2017-03-01
Crystal structure of WNK1 in complex with N-{(3R)-1-[(4-chlorophenyl)methyl]pyrrolidin-3-yl}-2-(3-methoxyphenyl)-N-methylquinoline-4-carboxamide (compound 8) (PDB entry 5WE8)
Macromolecule: Serine/threonine-protein kinase WNK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 279 residues
Sequence: GELETKAVGMSNDGRFLKFDIEIGRGSFKTVYKGLDTETTVEVAWCELQDRKLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWESTVKGKKCIVLVTELMTSGTLKTYLKRFKVMKIKVLRSWCRQILKGLQFLHTRTPPIIHRDLKCDNIFITGPTGSVKIGDLGLATLKRADFAKSVIGTPEFMAPEMYAAAYDESVDVYAFGMCMLEMATSEYPYSECQNAAQIYRRVTSGVKPASFDKVAIPEVKEIIEGCIRQNKDERYSIKDLLNHAFFQEET
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.006
R work: 0.2025
R free: 0.2466
Average B factor: 40.0299
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: co-crystallization of 10 mg/mL protein, 0.5 mM AMP-PNP, 1.5 mM manganese(II) chloride, 1 mM compound in
crystallization reservoir solution (100 mM HEPES, pH 7.5, 15-17% PEG3350, 100-300 mM calcium acetate)
Matthews coefficient: 2.14
Solvent content (%): 42.4
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2017-08-16
human carbonic anhydrase II in complex with ligand (PDB entry 5EH8)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.381
R work: 0.1503
R free: 0.1733
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 280
Crystal growth procedure: ammonium sulfate, tris chloride
Matthews coefficient: 2.08
Solvent content (%): 40.73
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: 2016-03-09
Crystal structure of the non-myristoylated mutant [L8K]Arf1 in complex with a GDP analogue (PDB entry 8SDW)
Macromolecule: ADP-ribosylation factor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 181 residues
Sequence: MGNIFANKFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.19
R free: 0.21
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.2 M Sodium nitrate, 20% w/v Polyethylene glycol 3,350, pH 6.8
Matthews coefficient: 2.17
Solvent content (%): 43.26
Ligand: GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE (G3D)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(28-30(18,19)20)3(27-9)1-26-32(24,25)29-31(21,22)23/h2-3,5-6,9,16H,1H2,(H,24,25)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
Release date: 2023-06-28
UFL1/DDRGK1 bound to UFC1 (PDB entry 8C0D)
Macromolecule: E3 UFM1-protein ligase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2
Sequence length: 194 residues
Sequence: MGHHHHHHENLYFQGMADAWEEIRRLAADFQRAQFAEATQRLSERNCIEIVNKLIAQKQLEVVHTLDGKEYITPAQISKEMRDELHVRGGRVNIVDLQQVINVDLIHIENRIGDIIKSEKHVQLVLGQLIDENYLDRLAEEVNDKLQESGQVTISELCKTYDLPGNFLTQALTQRLGRIISGHIDLDNRGVIFT
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.564
R work: 0.232
R free: 0.2858
Average B factor: 47.927
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 292
Crystal growth procedure: 0.1M HEPES, 1.03M Li2SO4
Matthews coefficient: 2.99
Solvent content (%): 58.91
Release date: 2023-12-27
Zn- Carbonic Anhydrase II pH 7.8 20 atm CO2 (PDB entry 6LUX)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1128
R free: 0.1418
Average B factor: 14.193
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.1
Solvent content (%): 41.36
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: 2020-08-19
Three dimensional structure of human carbonic anhydrase II in complex with 2-(But-2-yn-1-ylsulfamoyl)-4-sulfamoylbenzoic acid (PDB entry 5AML)
Macromolecule: CARBONIC ANHYDRASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 259 residues
Sequence: SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.36
R work: 0.11795
R free: 0.16114
Average B factor: 14.963
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 294
Crystal growth procedure: 1,54 M SODIUM CITRATE 60 MM TRIS- HCL, PH 9.0, PROTEIN 10 MG/ML 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, TIME 2-5 DAYS
Matthews coefficient: 2.1
Solvent content (%): 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: 2015-04-08
AKR1B1 at 1.65 MGy radiation dose. (PDB entry 6F82)
Macromolecule: Aldose reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.21
Sequence length: 316 residues
Sequence: MASRILLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.03
R work: 0.1097
R free: 0.139
Average B factor: 16
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 298
Crystal growth procedure: PEG 6000, AmCitrate
Matthews coefficient: 2.17
Solvent content (%): 43.28
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2019-03-13