satarupa22/MacromolecularLigandDB huggingface dataset:
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCH3, beta, gamma dTTP analogue (PDB entry 6CTJ)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 16 residues
Sequence: CCGACAGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1907
R free: 0.2572
Average B factor: 37.4867
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.14
Solvent content (%): 42.43
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-06-20
Crystal structure of human MTH1(G2K mutant) in complex with 2-oxo-dATP at pH 9.7 (PDB entry 8I1H)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 156 residues
Sequence: MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.18
R work: 0.1353
R free: 0.1656
Average B factor: 21.23
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: sodium citrate, caps, NaCl
Matthews coefficient: 1.9
Solvent content (%): 35.1
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2023-03-22
Rapid optimisation of fragments and hits to lead compounds from screening of crude reaction mixtures (PDB entry 6TMP)
Macromolecule: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.2
Sequence length: 394 residues
Sequence: GSAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDGSTNPAHPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVYNKSAWRHYQTIQEAGDWCVPSTEPKNTSTYRVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.076
R work: 0.1719
R free: 0.2401
Average B factor: 47.262
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Sodium acetate pH 5.8
0.125 M Magnesium chloride
Matthews coefficient: 3.23
Solvent content (%): 61.92
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2020-10-14
Crystal structure of CHK1-10pt-mutant complex with adenine (PDB entry 7BJE)
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): 1.8
R work: 0.1717
R free: 0.1988
Average B factor: 34.461
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: 2.31
Solvent content (%): 46.81
Ligand: ADENINE (ADE)
Ligand formula: C5 H5 N5
Ligand molecular weight: 135.127
Ligand SMILES: c1[nH]c2c(n1)c(ncn2)N
Ligand InChI: InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)
Release date: 2021-07-07
Peptide VPCGTAHE in complex with human cathepsin V C25A mutant (PDB entry 7Q8L)
Macromolecule: Cathepsin L2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.43
Sequence length: 222 residues
Sequence: DLPKSVDWRKKGYVTPVKNQKQCGSAWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRPQGNQGCNGGFMARAFQYVKENGGLDSEESYPYVAVDEICKYRPENSVAQDTGFTVVAPGKEKALMKAVATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVVGYGFEGANSQNSKYWLVKNSWGPEWGSNGYVKIAKDKNNHCGIATAASYPNV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1674
R free: 0.188
Average B factor: 46.36
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 77 % MPD, 23 % of 60 mM TRIS, pH 8
Matthews coefficient: 2.82
Solvent content (%): 56.37
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2022-11-23
Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2304 (PDB entry 8C7W)
Macromolecule: Activin receptor type I
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.207
R free: 0.2392
Average B factor: 32.59
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 1.6M ammonium sulfate, 0.1M tris pH 8.5, 4% glycerol
Matthews coefficient: 2.66
Solvent content (%): 53.86
Ligand: 6-methyl-9-piperazin-1-yl-4-(3,4,5-trimethoxyphenyl)-5,7-dihydropyrido[4,3-d][2]benzazepine (U0C)
Ligand formula: C27 H32 N4 O3
Ligand molecular weight: 460.568
Ligand SMILES: CN1Cc2cc(ccc2-c3cncc(c3C1)c4cc(c(c(c4)OC)OC)OC)N5CCNCC5
Ligand InChI: InChI=1S/C27H32N4O3/c1-30-16-19-11-20(31-9-7-28-8-10-31)5-6-21(19)23-15-29-14-22(24(23)17-30)18-12-25(32-2)27(34-4)26(13-18)33-3/h5-6,11-15,28H,7-10,16-17H2,1-4H3
Release date: 2023-02-08
Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203c) (PDB entry 6C01)
Macromolecule: Ectonucleotide pyrophosphatase/phosphodiesterase family member 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.1
Sequence length: 838 residues
Sequence: DRHHHHHHKLLEKQGSCRKKCFDASFRGLENCRCDVACKDRGDCCWDFEDTCVESTRIWMCNKFRCGETRLEASLCSCSDDCLQRKDCCADYKSVCQGETSWLEENCDTAQQSQCPEGFDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLSSKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGMDQTYCNKMEYMTDYFPRINFFYMYEGPAPRIRAHNIPHDFFSFNSEEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNVRIDKVHLFVDQQWLAVRSKSNTNCGGGNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPAPNNGTHGSLNHLLKVPFYEPSHAEEVSKFSVCGFANPLPTESLDCFCPHLQNSTQLEQVNQMLNLTQEEITATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGFGKAMRMPMWSSYTVPQLGDTSPLPPTVPDCLRADVRVPPSESQKCSFYLADKNITHGFLYPPASNRTSDSQYDALITSNLVPMYEEFRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYNYDGHFDAPDEITKHLANTDVPIPTHYFVVLTSCKNKSHTPENCPGWLDVLPFIIPHRPTNVESCPEGKPEALWVEERFTAHIARVRDVELLTGLDFYQDKVQPVSEILQLKTYLPTFETTI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1743
R free: 0.2138
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M buffer PCB (QIAGEN PACT suite), 25% PEG 1500
Matthews coefficient: 2.79
Solvent content (%): 55.87
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: 2018-05-02
Human Cathepsin-G Inhibited by S. aureus EapH1 (PDB entry 6VTM)
Macromolecule: Cathepsin G
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.20
Sequence length: 224 residues
Sequence: IIGGRESRPHSRPYMAYLQIQSPAGQSRCGGFLVREDFVLTAAHCWGSNINVTLGAHNIQRRENTQQHITARRAIRHPQYNQRTIQNDIMLLQLSRRVRRNRNVNPVALPRAQEGLRPGTLCTVAGWGRVSMRRGTDTLREVQLRVQRDRQCLRIFGSYDPRRQICVGDRRERKAAFKGDSGGPLLCNNVAHGIVSYGKSSGVPPEVFTRVSSFLPWIRTTMRS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.174
R free: 0.209
Average B factor: 22.33
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M lithium sulfate monohydrate, 0.1 M Tris, pH 8.5, 25% w/v PEG3350
Matthews coefficient: 2.28
Solvent content (%): 46.09
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: 2020-04-22
Crystal structure of human Butyrylcholinesterase in complex with N-((2S,3R)-4-((2,2-dimethylpropyl)amino)-3-hydroxy-1-phenylbutan-2-yl)-2,2-diphenylacetamide (PDB entry 7AMZ)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 529 residues
Sequence: EDDIIIATKNGKVRGMQLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDQYTKAEEILSRSIVKRWANFAKYGNPQETQNQSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1974
R free: 0.2199
Average B factor: 54.47
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate
Matthews coefficient: 3.19
Solvent content (%): 61.48
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: 2021-05-26
Crystal structure of the open conformation of Angiotensin-1 converting enzyme N-domain. (PDB entry 6ZPQ)
Macromolecule: Angiotensin-converting enzyme
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1
Sequence length: 629 residues
Sequence: LDPGLQPGQFSADEAGAQLFAQSYQSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQQFTDPQLRRIIGAVRTLGSANLPLAKRQQYNALLSQMSRIYSTAKVCLPQKTATCWSLDPDLTNILASSRSYAMLLFAWEGWHNAAGIPLKPLYEDFTALSNEAYKQDGFTDTGAYWRSWYNSPTFEDDLEHLYQQLEPLYLNLHAFVRRALHRRYGDRYINLRGPIPAHLLGDMWAQSWENIYDMVVPFPDKPNLDVTSTMLQQGWQATHMFRVAEEFFTSLELSPMPPEFWEGSMLEKPADGREVVCHASAWDFYNRKDFRIKQCTRVTMDQLSTVHHEMGHIQYYLQYKDLPVSLRRGANPGFHEAIGDVLALSVSTPEHLHKIGLLDRVTNDTESDINYLLKMALEKIAFLPFGYLVDQWRWGVFSGRTPPSRYNFDWWYLRTKYQGICPPVTRNETHFDAGAKFHVPNVTPYIRYFVSFVLQFQFHEALCKEAGYEGPLHQCDIYRSTKAGAKLRKVLRAGSSRPWQEVLKDMVGLDALDAQPLLKYFQLVTQWLQEQNQQNGEVLGWPEYQWHPPLPDNYPEGIDLVTDEAEASKFVEEYDL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1844
R free: 0.2136
Average B factor: 43.45
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.1 M Tris/Bicine pH 8.5, 0.06 M Divalent Cations, 30% PEG550MME/PEG20000
Matthews coefficient: 3.05
Solvent content (%): 59.72
Ligand: BICINE (BCN)
Ligand formula: C6 H13 N O4
Ligand molecular weight: 163.172
Ligand SMILES: C(CO)N(CCO)CC(=O)O
Ligand InChI: InChI=1S/C6H13NO4/c8-3-1-7(2-4-9)5-6(10)11/h8-9H,1-5H2,(H,10,11)
Release date: 2020-10-28
Crystal structure of human carbonic anhydrase isozyme II with inhibitor (PDB entry 4PYY)
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): 1.75
R work: 0.149
R free: 0.2
Average B factor: 15.231
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Matthews coefficient: 2.04
Solvent content (%): 39.2
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: 2015-01-28
Crystal structure of EP300 HAT domain in complex with compound (+)-3 (PDB entry 7VHY)
Macromolecule: Histone acetyltransferase p300
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 454 residues
Sequence: GPSLGYCCGRKLEFSPQTLCCYGKQLCTIPRDATYYSYQNRYHFCEKCFNEIQGESVSLGDDPSQPQTTINKEQFSKRKNDTLDPELFVECTECGRKMHQICVLHHEIIWPAGFVCDGCLKKSARTRKENKFSAKRLPSTRLGTFLENRVNDFLRRQNHPESGEVTVRVVHASDKTVEVKPGMKARFVDSGEMAESFPYRTKALFAFEEIDGVDLCFFGMHVQEYGSDCPPPNQRRVYISYLDSVHFFRPKCLRTAVYHEILIGYLEYVKKLGYTTGHIWACPPSEGDDYIFHCHPPDQKIPKPKRLQEWFKKMLDKAVSERIVHDYKDIFKQATEDRLTSAKELPYFEGDFWPNVLEESIKESGGSGSQKLYATMEKHKEVFFVIRLIAGPAANSLPPIVDPDPLIPCDLMDGRDAFLTLARDKHLEFSSLRRAQWSTMCMLVELHTQSQDRF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2122
R free: 0.2502
Average B factor: 54.7465
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 15% PEG3350, 0.1 M HEPES (pH7.0)
Matthews coefficient: 2.99
Solvent content (%): 58.87
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: 2022-04-27
Pre-catalytic Ternary Complex of Human DNA Polymerase Mu with Templating Adenine and Incoming Ca-8oxodGTP (PDB entry 6AK8)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.17401
R free: 0.20082
Average B factor: 26.93
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES pH 7.5, 18% PEG4000
Matthews coefficient: 2.68
Solvent content (%): 54.07
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: 2019-05-29
Human Carbonic Anhydrase II bound tert-butyl (3-(4-(3-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)propoxy)butoxy)propyl)carbamate (PDB entry 8EXC)
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): 1.9
R work: 0.1768
R free: 0.2267
Average B factor: 23.77
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 2.6-3.0 M Ammonium sulfate in 50 mM Tris-Sulfate (pH 8)
Matthews coefficient: 2.08
Solvent content (%): 40.98
Ligand: N-(3-{4-[3-({2-[(3R)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}amino)propoxy]butoxy}propyl)-4-sulfamoylbenzamide (X2U)
Ligand formula: C30 H37 N5 O9 S
Ligand molecular weight: 643.708
Ligand SMILES: c1cc2c(c(c1)NCCCOCCCCOCCCNC(=O)c3ccc(cc3)S(=O)(=O)N)C(=O)N(C2=O)C4CCC(=O)NC4=O
Ligand InChI: InChI=1S/C30H37N5O9S/c31-45(41,42)21-10-8-20(9-11-21)27(37)33-15-5-19-44-17-2-1-16-43-18-4-14-32-23-7-3-6-22-26(23)30(40)35(29(22)39)24-12-13-25(36)34-28(24)38/h3,6-11,24,32H,1-2,4-5,12-19H2,(H,33,37)(H2,31,41,42)(H,34,36,38)/t24-/m1/s1
Release date: 2023-02-22
Human endothelin receptor type-B in complex with antagonist K-8794 (PDB entry 5X93)
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: GGGLAPAEVPKGDRTAGSPPRTISPPPCQGPIEIKETFKYINTVVSCLVFVLGIIGNSTLLYIIYKNKCMRNGPNILIASLALGDLLHIVIAIPINVYKLLAEDWPFGAEMCKLVPFIQKASVGITVLSLCALSIDRYRAVASWSRIKGIGVPKWTAVEIVLIWVVSVVLAVPEAIGFDIITMDYKGSYLRICLLHPVQKTAFMQFYATAKDWWLFSFYFCLPLAITAFFYTLMTCEMLRKNIFEMLRIDEGGGSGGDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYLNDHLKQRREVAKTVFCLVLVFALCWLPLHLARILKLTLYNQNDPNRCELLSFLLVLDYIGINMASLNSCANPIALYLVSKRFKNAFKSALCCWAQSPSSENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2106
R free: 0.2387
Average B factor: 57.1766
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: PEG 500 DME, (NH4)2SO4, MOPS
Matthews coefficient: 2.84
Solvent content (%): 56.75
Ligand: 3-[6-[(4-tert-butylphenyl)sulfonylamino]-5-(2-methoxyphenoxy)-2-pyrimidin-2-yl-pyrimidin-4-yl]oxy-N-(2,6-dimethylphenyl)propanamide (K87)
Ligand formula: C36 H38 N6 O6 S
Ligand molecular weight: 682.789
Ligand SMILES: Cc1cccc(c1NC(=O)CCOc2c(c(nc(n2)c3ncccn3)NS(=O)(=O)c4ccc(cc4)C(C)(C)C)Oc5ccccc5OC)C
Ligand InChI: InChI=1S/C36H38N6O6S/c1-23-11-9-12-24(2)30(23)39-29(43)19-22-47-35-31(48-28-14-8-7-13-27(28)46-6)32(40-34(41-35)33-37-20-10-21-38-33)42-49(44,45)26-17-15-25(16-18-26)36(3,4)5/h7-18,20-21H,19,22H2,1-6H3,(H,39,43)(H,40,41,42)
Release date: 2017-08-16
Crystal structure of human USP2 in complex with ubiquitin and 6-thioguanine (PDB entry 5XU8)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 356 residues
Sequence: MNSKSAQGLAGLRNLGNTCFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELASPPSRMLEHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.17854
R free: 0.23827
Average B factor: 39.95
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 295
Crystal growth procedure: 24.5% PEG3350, 0.2 M MgC12, 0.1 M Bis-Tris
Matthews coefficient: 1.96
Solvent content (%): 37.18
Ligand: 2-amino-1,9-dihydro-6H-purine-6-thione (DX4)
Ligand formula: C5 H5 N5 S
Ligand molecular weight: 167.192
Ligand SMILES: c1[nH]c2c(n1)C(=S)NC(=N2)N
Ligand InChI: InChI=1S/C5H5N5S/c6-5-9-3-2(4(11)10-5)7-1-8-3/h1H,(H4,6,7,8,9,10,11)
Release date: 2018-02-28
Atomic resolution structure of human RNase 6 in the presence of phosphate anions in P21 space group. (PDB entry 6ENP)
Macromolecule: Ribonuclease K6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27
Sequence length: 128 residues
Sequence: MWPKRLTKAHWFEIQHIQPSPLQCNRAMSGINNYTQHCKHQNTFLHDSFQNVAAVCDLLSIVCKNRRHNCHQSSKPVNMTDCRLTSGKYPQCRYSAAAQYKFFIVACDPPQKSDPPYKLVPVHLDSIL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.042
R work: 0.1215
R free: 0.1449
Average B factor: 19.33
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 1 M ammonium phosphate, 100 mM sodium acetate pH 4.5
Matthews coefficient: 1.79
Solvent content (%): 31.16
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: 2018-10-24
Anti-FX Fab of mim8 in complex with human FXa (PDB entry 7AHU)
Macromolecule: Anti-FX Fab of mim8 light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 216 residues
Sequence: EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGQSSRTRGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQFGDSQLFTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2027
R free: 0.2633
Average B factor: 46.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M sodium acetate, 0.1 M sodium cacodylate, pH 6.5, 18 % (w/v) PEG 8000
Matthews coefficient: 2.97
Solvent content (%): 58.64
Ligand: L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide (0GJ)
Ligand formula: C14 H28 Cl N6 O5
Ligand molecular weight: 395.862
Ligand SMILES: C(CC(C(CCl)O)NC(=O)CNC(=O)C(CCC(=O)O)N)CNC(=[NH2+])N
Ligand InChI: InChI=1S/C14H27ClN6O5/c15-6-10(22)9(2-1-5-19-14(17)18)21-11(23)7-20-13(26)8(16)3-4-12(24)25/h8-10,22H,1-7,16H2,(H,20,26)(H,21,23)(H,24,25)(H4,17,18,19)/p+1/t8-,9-,10+/m0/s1
Release date: 2021-07-07
Crystal Structure of 1,5-dimethylindoline-2,3-dione covalently bound to the PH domain of Bruton's tyrosine kinase mutant R28C (PDB entry 6YYK)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 169 residues
Sequence: AAVILESIFLKRSQQKKKTSPLNFKKCLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEKITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEELRKRWIHQLKNVIRYNSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILEN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.2275
R free: 0.2964
Average B factor: 67.47
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M TRIS 8.5 pH, 32.5% w/v PEG 3350, 200mM MgCl2 500 mM NaCl
Matthews coefficient: 2.1
Solvent content (%): 41.55
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: 2021-05-12