satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human carbonic anhydrase isozyme II with 3-{[(4-methyl-6-oxo-1,6-dihydropyrimidin-2-yl)thio]acetyl}benzenesulfonamide (PDB entry 4QSB)
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): 1.4
R work: 0.188
R free: 0.22
Average B factor: 16.535
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 2.2M sodium malonate pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Matthews coefficient: 2.05
Solvent content (%): 39.99
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
Crystal structure of TL11-128 bound to TAK1-TAB1 (PDB entry 5JK3)
Macromolecule: Mitogen-activated protein kinase kinase kinase 7,TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 314 residues
Sequence: SLHMIDYKEIEVEEVVGRGAFGVVCKAKWRAKDVAIKQIESESERKAFIVELRQLSRVNHPNIVKLYGACLNPVCLVMEYAEGGSLYNVLHGAEPLPYYTAAHAMSWCLQCSQGVAYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICDFGTACDIQTHMTNNKGSAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDEIGGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQHSLPPGEDGRVEPYVDFAEFYRLWSVDHGEQSVVTAP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.371
R work: 0.2348
R free: 0.2658
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.65-0.75 M sodium citrate, 0.2 M NaCl, 0.1 M Tris, and 5mM adenosine. Adenosine bound TAK1-TAB1 crystals are backsoaked with inhibitor, pH 7.0
Matthews coefficient: 3.96
Solvent content (%): 68.91
Ligand: ~{N}-[2-[5-chloranyl-2-[(1-methylpyrazol-4-yl)amino]pyrimidin-4-yl]oxyphenyl]prop-2-enamide (6L4)
Ligand formula: C17 H15 Cl N6 O2
Ligand molecular weight: 370.793
Ligand SMILES: Cn1cc(cn1)Nc2ncc(c(n2)Oc3ccccc3NC(=O)C=C)Cl
Ligand InChI: InChI=1S/C17H15ClN6O2/c1-3-15(25)22-13-6-4-5-7-14(13)26-16-12(18)9-19-17(23-16)21-11-8-20-24(2)10-11/h3-10H,1H2,2H3,(H,22,25)(H,19,21,23)
Release date: 2017-02-15
Crystal structure of METTL9 in complex with SLC39A5 peptide and SAH (PDB entry 7Y9C)
Macromolecule: Protein-L-histidine N-pros-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 275 residues
Sequence: HMAAGGRKENHQWYVCNREKLCESLQAVFVQSYLDQGTQIFLNNSIEKSGWAAIQAYHSAVSSAFSLAMSRTSINGLLGRGSMFVFSPDQFQRLLKINPDWKTHRLLDLGAGDGEVTKIMSPHFEEIYATELSETMIWQLQKKKYRVLGINEWQNTGFQYDVISCLNLLDRCDQPLTLLKDIRSVLEPTRGRVILALVLPFHPYVENVGGKWEKPSEILEIKGQNWEEQVNSLPEVFRKAGFVIEAFTRLPYLCEGDMYNDYYVLDDAVFVLKPV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.192
R free: 0.2427
Average B factor: 28.5783
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES monohydrate pH6.5, 12 % w/v PEG 20000, 0.2 M sodium thiocyanate
Matthews coefficient: 2.26
Solvent content (%): 45.46
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: 2023-04-12
Crystal structure of cysteine-bound ferrous form of the crosslinked Cl-Tyr157 human cysteine dioxygenase (PDB entry 6CDN)
Macromolecule: Cysteine dioxygenase type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.20
Sequence length: 200 residues
Sequence: SEQTEVLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKETLFAWPDKKSNEMVKKSERVLRENQCAYINDSVGLHRVENISHTEPAVSLHLXSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTPNATSGSLENN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.055
R work: 0.1621
R free: 0.1928
Average B factor: 37.4611
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M MES, 2 M ammonium sulfate, 2% PEG400
Matthews coefficient: 3.69
Solvent content (%): 66.7
Ligand: CYSTEINE (CYS)
Ligand formula: C3 H7 N O2 S
Ligand molecular weight: 121.158
Ligand SMILES: C(C(C(=O)O)N)S
Ligand InChI: InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1
Release date: 2018-07-04
Human Carbonic Anhydrase II in complex with fluorinated benzenesulfonamide (PDB entry 6S9G)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 265 residues
Sequence: GSPEFMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.14
R work: 0.1229
R free: 0.1471
Average B factor: 15.82
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium sulfate 2.7 M, TRIS 0.1 M, saturated with para-Chloromercuribenzoic acid
Matthews coefficient: 2.06
Solvent content (%): 40.27
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: 2020-04-15
Crystal structure of the catalytic domain of human JARID1B in complex with L-2-hydroxyglutarate (PDB entry 5FZD)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1955
R free: 0.235
Crystallization pH: 7.5
Crystal growth procedure: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC
Matthews coefficient: 2.1
Solvent content (%): 41.57
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: 2017-03-22
Crystal structure of the human bromodomain of CREBBP bound to the inhibitor XDM4 (PDB entry 5NRW)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2193
R free: 0.2599
Average B factor: 17.886
Crystallization method: EVAPORATION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: LiSO4, PEG 3350, ethylene glycol
Matthews coefficient: 2.25
Solvent content (%): 45.42
Ligand: 4-ethanoyl-3-ethyl-5-methyl-~{N}-(naphthalen-1-ylmethyl)-1~{H}-pyrrole-2-carboxamide (96N)
Ligand formula: C21 H22 N2 O2
Ligand molecular weight: 334.412
Ligand SMILES: CCc1c(c([nH]c1C(=O)NCc2cccc3c2cccc3)C)C(=O)C
Ligand InChI: InChI=1S/C21H22N2O2/c1-4-17-19(14(3)24)13(2)23-20(17)21(25)22-12-16-10-7-9-15-8-5-6-11-18(15)16/h5-11,23H,4,12H2,1-3H3,(H,22,25)
Release date: 2017-08-16
DYRK1A in complex with XMD14-124 (PDB entry 6EIQ)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 368 residues
Sequence: GASDSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADEGTNTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.21812
R free: 0.25245
Average B factor: 55.491
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M KSCN; 0.1M NaCl; 12% PEG 3350, pH 6.8
Matthews coefficient: 2.57
Solvent content (%): 52.22
Ligand: [4-azanyl-2-[[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino]-1,3-thiazol-5-yl]-phenyl-methanone (B6Z)
Ligand formula: C22 H25 N5 O2 S
Ligand molecular weight: 423.531
Ligand SMILES: CN1CCN(CC1)c2ccc(c(c2)OC)Nc3nc(c(s3)C(=O)c4ccccc4)N
Ligand InChI: InChI=1S/C22H25N5O2S/c1-26-10-12-27(13-11-26)16-8-9-17(18(14-16)29-2)24-22-25-21(23)20(30-22)19(28)15-6-4-3-5-7-15/h3-9,14H,10-13,23H2,1-2H3,(H,24,25)
Release date: 2018-08-29
Binary Complex of Human DNA Polymerase Mu with MgdCTP (PDB entry 6IPM)
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): 1.72
R work: 0.20448
R free: 0.23632
Average B factor: 21.806
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M HEPES pH 7.5, 1.5 M Li2SO4
Matthews coefficient: 2.45
Solvent content (%): 49.76
Ligand: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE (DCP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
Release date: 2019-05-29
The structure of Artemis/SNM1C/DCLRE1C with 2 Zinc ions (PDB entry 7AF1)
Macromolecule: Protein artemis
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 362 residues
Sequence: SMSSFEGQMAEYPTISIDRFDRENLRARAYFLSHCHKDHMKGLRAPTLKRRLECSLKVYLYCSPVTKELLLTSPKYRFWKKRIISIEIETPTQISLVDEASGEKEEIVVTLLPAGHCPGSVMFLFQGNNGTVLYTGDFRLAQGEAARMELLHSGGRVKDIQSVYLDTTFCDPRFYQIPSREECLSGVLELVRSWITRSPYHVVWLNCKAAYGYEYLFTNLSEELGVQVHVNKLDMFRNMPEILHHLTTDRNTQIHACRHPKAEEYFQWSKLPCGITSRNRIPLHIISIKPSTMWFGERSRKTNVIVRTGESSYRACFSFHSSYSEIKDFLSYLCPVNAYPNVIPVGTTMDKVVEILKPLCRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.19051
R free: 0.21169
Average B factor: 20.143
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 20% PEG 3350 0.3 M Ammonium Chloride
Matthews coefficient: 1.19
Solvent content (%): 35.52
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: 2020-10-28
The Crystal Structure of human neuropeptide Y Y1 receptor with UR-MK299 (PDB entry 5ZBQ)
Macromolecule: Neuropeptide Y receptor type 1,T4 Lysozyme
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 525 residues
Sequence: NSTLFSQVENHSVHSNFSEKNAQLLAFENDDCHLPLAMIFTLALAYGAVIILGVSGNLALIIIILKQKEMRNVTNILIVNLSFSDLLVAIMCLPFTFVYTLMDHWVFGEAMCKLNPFVQCVSITVSIWSLVLIAVERHQLIINPRGWRPNNRHAYVGIAVIWVLAVASSLPFLIYQVMTDEPFQNVTLDAYKDKYVCFDQFPSDSHRLSYTTLLLVLQYFGPLCFIFICYFKIYIRLKRRNNMMDKMRDNKYRSSETKRINIMLLSIVVAFAVCWLPLTIFNTVFDWNHQIIATCNHNLLFLLCHLTAMISTCVNPIFYGFLNKNFQRDLQFFFNFCDFRSRDDDYETIAMSTMHTDEFLEVLFQNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.225
R free: 0.247
Average B factor: 87.93
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris, pH 7.4-8.0, 30-40% (v/v) PEG400, 50-150 mM sodium tartrate and 100 uM UR-MK299
Matthews coefficient: 2.58
Solvent content (%): 52.34
Ligand: N~2~-(diphenylacetyl)-N-[(4-hydroxyphenyl)methyl]-N~5~-(N'-{[2-(propanoylamino)ethyl]carbamoyl}carbamimidoyl)-D-ornithinamide (9AO)
Ligand formula: C33 H41 N7 O5
Ligand molecular weight: 615.723
Ligand SMILES: CCC(=O)NCCNC(=O)N=C(N)NCCCC(C(=O)NCc1ccc(cc1)O)NC(=O)C(c2ccccc2)c3ccccc3
Ligand InChI: InChI=1S/C33H41N7O5/c1-2-28(42)35-20-21-37-33(45)40-32(34)36-19-9-14-27(30(43)38-22-23-15-17-26(41)18-16-23)39-31(44)29(24-10-5-3-6-11-24)25-12-7-4-8-13-25/h3-8,10-13,15-18,27,29,41H,2,9,14,19-22H2,1H3,(H,35,42)(H,38,43)(H,39,44)(H4,34,36,37,40,45)/t27-/m1/s1
Release date: 2018-04-25
Human carbonic anhydrase II (F131W) complexed with benzo[d]thiazole-2-sulfonamide (PDB entry 5JDV)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 258 residues
Sequence: HHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDWGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.34
R work: 0.1364
R free: 0.1694
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: We soaked these crystals with BTA and TA 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
Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 35-42 (PDB entry 5AMB)
Macromolecule: ANGIOTENSIN-CONVERTING ENZYME
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.15.1
Sequence length: 629 residues
Sequence: LDPGLQPGQFSADEAGAQLFAQSYQSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQQFTDPQLRRIIGAVRTLGSANLPLAKRQQYNALLSQMSRIYSTAKVCLPQKTATCWSLDPDLTNILASSRSYAMLLFAWEGWHNAAGIPLKPLYEDFTALSNEAYKQDGFTDTGAYWRSWYNSPTFEDDLEHLYQQLEPLYLNLHAFVRRALHRRYGDRYINLRGPIPAHLLGDMWAQSWENIYDMVVPFPDKPNLDVTSTMLQQGWQATHMFRVAEEFFTSLELSPMPPEFWEGSMLEKPADGREVVCHASAWDFYNRKDFRIKQCTRVTMDQLSTVHHEMGHIQYYLQYKDLPVSLRRGANPGFHEAIGDVLALSVSTPEHLHKIGLLDRVTNDTESDINYLLKMALEKIAFLPFGYLVDQWRWGVFSGRTPPSRYNFDWWYLRTKYQGICPPVTRNETHFDAGAKFHVPNVTPYIRYFVSFVLQFQFHEALCKEAGYEGPLHQCDIYRSTKAGAKLRKVLRAGSSRPWQEVLKDMVGLDALDAQPLLKYFQLVTQWLQEQNQQNGEVLGWPEYQWHPPLPDNYPEGIDLVTDEAEASKFVEEYDL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1575
R free: 0.18115
Crystallization pH: 8.5
Crystal growth procedure: 0.06 M DIVALENT CATIONS, 0.1 M TRIS/ BICINE PH 8.5, 30 % PEG550MME/PEG20000
Matthews coefficient: 2.85
Solvent content (%): 57
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: 2016-01-13
Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor (S)-2-(((1r,4S)-4-(4-amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclohexyl)amino)-N,4-dimethylpentanamide (PDB entry 5H0G)
Macromolecule: Tyrosine-protein kinase HCK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 454 residues
Sequence: GAMGSGIRIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLETEEWFFKGISRKDAERQLLAPGNMLGSFMIRDSETTKGSYSLSVRDYDPRQGDTVKHYKIRTLDNGGFYISPRSTFSTLQELVDHYKKGNDGLCQKLSVPCMSSKPQKPWEKDAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPGSMSVEAFLAEANVMKTLQHDKLVKLHAVVTKEPIYIITEFMAKGSLLDFLKSDEGSKQPLPKLIDFSAQIAEGMAFIEQRNYIHRDLRAANILVSASLVCKIADFGLARVIEDNEYTAREGAKFPIKWTAPEAINFGSFTIKSDVWSFGILLMEIVTYGRIPYPGMSNPEVIRALERGYRMPRPENCPEELYNIMMRCWKNRPEERPTFEYIQSVLDDFYTATESQYEEIP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.181
R free: 0.2236
Average B factor: 37.1622
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.22-0.25 M ammonium formate, 12-22 % PEG 3350
Matthews coefficient: 2.32
Solvent content (%): 46.93
Ligand: (2~{S})-2-[[4-[4-azanyl-5-(4-phenoxyphenyl)pyrrolo[2,3-d]pyrimidin-7-yl]cyclohexyl]amino]-~{N},4-dimethyl-pentanamide (OOU)
Ligand formula: C31 H38 N6 O2
Ligand molecular weight: 526.672
Ligand SMILES: CC(C)CC(C(=O)NC)NC1CCC(CC1)n2cc(c3c2ncnc3N)c4ccc(cc4)Oc5ccccc5
Ligand InChI: InChI=1S/C31H38N6O2/c1-20(2)17-27(31(38)33-3)36-22-11-13-23(14-12-22)37-18-26(28-29(32)34-19-35-30(28)37)21-9-15-25(16-10-21)39-24-7-5-4-6-8-24/h4-10,15-16,18-20,22-23,27,36H,11-14,17H2,1-3H3,(H,33,38)(H2,32,34,35)/t22-,23-,27-/m0/s1
Release date: 2017-10-04
The crystal structure of CK2alpha in complex with compound 11 (PDB entry 5OS8)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1765
R free: 0.201
Average B factor: 20.77
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 1.95
Solvent content (%): 36.96
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2018-02-28
The structure of human mitochondrial methyltransferase METTL15 with RBFA and SAM (PDB entry 8IPL)
Macromolecule: Putative ribosome-binding factor A, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 34 residues
Sequence: TTEPTTSSSLCGIDHEALNKQIMEYKRRKDKGLG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1799
R free: 0.2346
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 17% w/v PEG 4000, 0.05M Potassium chloride, 0.1M Lithium chloride, 0.012M Spermine tetrahydrochloride, 0.05M MES PH6.5
Matthews coefficient: 2.05
Solvent content (%): 39.9
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: 2024-01-03
KRAS-G12V in complex with BI-2865 (PDB entry 8AZZ)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.02
R work: 0.145
R free: 0.1669
Average B factor: 22.96
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2mM Magnesium Chloride, 20% PEG 2000, 100mM sodium acetate pH 4.4
Matthews coefficient: 2.55
Solvent content (%): 51.69
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2023-06-21
Crystal structure of the cholecystokinin receptor CCKAR in complex with lintitript (PDB entry 7F8U)
Macromolecule: Fusion protein of Cholecystokinin receptor type A and Endolysin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 534 residues
Sequence: DYKDDDDGAPDVVDSLLVNGSNITPPCELGLENETLFCLDQPRPSKEWQPAVQILLYSLIFLLSVLGNTLVITVLIRNKRMRTVTNIFLLSLAVSNLMLCLFCMPFNLIPNLLKDFIFGSAVCKTTTYFMGTSVSVSTWNLVAISLERYGAICKPLQSRVWQTKSHALKVIAATWCLSFTIMTPYPIYSNLVPFTKNNNQTANMCRFLLPNDVMQQSWHTFLLLILFLIPGIVMMVAYGLISLELYQGINIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYAANLMAKKRVIRMLIVIVVLFFLCWMPIFSANAWRAYDTASAERRLSGTPISFILLLSYTSSCVNPIIYCFMNKRFRLGFMATFPCCPNPGPPGARGEVGEEEEGEFLEVLFQGPHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.236
R free: 0.253
Average B factor: 91.14
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, pH7.5, 25% PEG400, 250 mM sodium tartrate ,1% 1,2 -butanediol
Matthews coefficient: 2.74
Solvent content (%): 55.04
Ligand: 2-[2-[[4-(2-chlorophenyl)-1,3-thiazol-2-yl]carbamoyl]indol-1-yl]ethanoic acid (1OE)
Ligand formula: C20 H14 Cl N3 O3 S
Ligand molecular weight: 411.861
Ligand SMILES: c1ccc2c(c1)cc(n2CC(=O)O)C(=O)Nc3nc(cs3)c4ccccc4Cl
Ligand InChI: InChI=1S/C20H14ClN3O3S/c21-14-7-3-2-6-13(14)15-11-28-20(22-15)23-19(27)17-9-12-5-1-4-8-16(12)24(17)10-18(25)26/h1-9,11H,10H2,(H,25,26)(H,22,23,27)
Release date: 2021-10-13