satarupa22/MacromolecularLigandDB huggingface dataset:
Fragment-based discovery of a highly potent, orally bioavailable inhibitor which modulates the phosphorylation and catalytic activity of ERK1/2 (PDB entry 6GDM)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.18204
R free: 0.24265
Average B factor: 33.486
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 35.0%w/v MPEG 2000, 0.2M (NH4)2SO4, 0.1M HEPES/NaOHpH=7.2, 0.02M Mercaptoethanol
Matthews coefficient: 2.3
Solvent content (%): 46.54
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: 2018-05-30
DNA Polymerase Lambda, dCTP:At Mn2+ Reaction State Ternary Complex, 225 min (PDB entry 7M4H)
Macromolecule: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 11 residues
Sequence: CGGCAGTACTG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.923
R work: 0.1923
R free: 0.2275
Average B factor: 46.8253
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.85
Solvent content (%): 56.79
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2022-07-06
Bruton's tyrosine kinase (BTK) with pyridazinone compound 9 (PDB entry 5KUP)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 271 residues
Sequence: MGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.389
R work: 0.1655
R free: 0.1772
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 286
Crystal growth procedure: PEG 10K, citrate, LiSO4
Matthews coefficient: 2.26
Solvent content (%): 45.67
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: 2016-09-14
BACE-1 in complex with compound #32 (PDB entry 6UWP)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 442 residues
Sequence: MAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.1343
R free: 0.1546
Average B factor: 16.661
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 100mM Sodium Cacodylate pH 7.4, 12% PEG 8K, 200mM Ammonium Sulfate
Matthews coefficient: 2.6
Solvent content (%): 52.65
Ligand: (1R,2R)-2-[(4aR,7aR)-2-amino-6-(pyrimidin-2-yl)-4a,5,6,7-tetrahydropyrrolo[3,4-d][1,3]thiazin-7a(4H)-yl]-N-{[(1R,2R)-2-methylcyclopropyl]methyl}cyclopropane-1-carboxamide (QKA)
Ligand formula: C19 H26 N6 O S
Ligand molecular weight: 386.514
Ligand SMILES: CC1CC1CNC(=O)C2CC2C34CN(CC3CSC(=N4)N)c5ncccn5
Ligand InChI: InChI=1S/C19H26N6OS/c1-11-5-12(11)7-23-16(26)14-6-15(14)19-10-25(18-21-3-2-4-22-18)8-13(19)9-27-17(20)24-19/h2-4,11-15H,5-10H2,1H3,(H2,20,24)(H,23,26)/t11-,12+,13+,14-,15-,19+/m1/s1
Release date: 2019-12-11
Crystal structure of human MTH1 in complex with compound MI1030 (PDB entry 6JVT)
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: MGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.801
R work: 0.1865
R free: 0.2301
Average B factor: 23.1269
Crystallization method: EVAPORATION
Crystallization pH: 3.75
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG 6000, 200 mM Lithium sulphate, 100 mM Sodium acetate pH 3.75
Matthews coefficient: 2.27
Solvent content (%): 45.84
Ligand: N4-methyl-6-[4-(oxetan-3-yl)piperazin-1-yl]pyrimidine-2,4-diamine (CJR)
Ligand formula: C12 H20 N6 O
Ligand molecular weight: 264.327
Ligand SMILES: CNc1cc(nc(n1)N)N2CCN(CC2)C3COC3
Ligand InChI: InChI=1S/C12H20N6O/c1-14-10-6-11(16-12(13)15-10)18-4-2-17(3-5-18)9-7-19-8-9/h6,9H,2-5,7-8H2,1H3,(H3,13,14,15,16)
Release date: 2020-10-28
Crystal structure of Rev7-R124A/Rev3-RBM2 (residues 1988-2014) complex (PDB entry 6BC8)
Macromolecule: Mitotic spindle assembly checkpoint protein MAD2B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 227 residues
Sequence: MGSSHHHHHHSQDPNSMTTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPELNQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVEQLLAAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVHMHDPRLIPLKTMTSDILKMQLYVEERAHKGS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.68
R work: 0.181
R free: 0.223
Average B factor: 47.572
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 292.15
Crystal growth procedure: well solution containing 100 mM sodium acetate, 200 mM NaCl, 1.4 M ammonium sulfate was mixed at 1:1 ratio with protein at 45 mg/mL in 5 mM HEPES, 100 mM NaCl, 10 mM DTT, pH=7.4
Matthews coefficient: 2.32
Solvent content (%): 46.92
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: 2018-08-01
Crystal structure of human carbonic anhydrase isozyme II with inhibitor (PDB entry 4QJM)
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: 0.161
R free: 0.212
Average B factor: 17.018
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M sodium BICINE pH 9, 0.2M ammonium sulfate, 2M sodium malonate pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Matthews coefficient: 2.02
Solvent content (%): 38.6
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: 2015-04-15
FACTOR XIA IN COMPLEX WITH THE INHIBITOR trans-N-{(1S)-1-[4-(3-amino-2H-indazol-6-yl)pyridin-2-yl]-2-phenylethyl}-4-(aminomethyl)cyclohexanecarboxamide (PDB entry 4WXI)
Macromolecule: COAGULATION FACTOR XI, LIGHT CHAIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1764
R free: 0.2261
Average B factor: 22.37
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 100 MM SODIUM ACETATE, PH 4.6, 26%(w/v) MEPEG2000, 200 MM AMMONIUM SULFATE
Matthews coefficient: 3.48
Solvent content (%): 64.61
Ligand: trans-N-{(1S)-1-[4-(3-amino-2H-indazol-6-yl)pyridin-2-yl]-2-phenylethyl}-4-(aminomethyl)cyclohexanecarboxamide (3VM)
Ligand formula: C28 H32 N6 O
Ligand molecular weight: 468.593
Ligand SMILES: c1ccc(cc1)CC(c2cc(ccn2)c3ccc4c(c3)n[nH]c4N)NC(=O)C5CCC(CC5)CN
Ligand InChI: InChI=1S/C28H32N6O/c29-17-19-6-8-20(9-7-19)28(35)32-26(14-18-4-2-1-3-5-18)25-16-22(12-13-31-25)21-10-11-23-24(15-21)33-34-27(23)30/h1-5,10-13,15-16,19-20,26H,6-9,14,17,29H2,(H,32,35)(H3,30,33,34)/t19-,20-,26-/m0/s1
Release date: 2015-01-28
Binary complex crystal structure of DNA polymerase Beta with T:T mismatch at the primer terminus (PDB entry 5J0Y)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.189
R free: 0.2448
Average B factor: 24.8978
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
Matthews coefficient: 2.41
Solvent content (%): 48.98
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2016-10-26
Crystal Structure of AKR1C3 complexed with CAPE (PDB entry 5HNT)
Macromolecule: Aldo-keto reductase family 1 member C3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.357
Sequence length: 315 residues
Sequence: QCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKKAQLDYVDLYLIHSPMSLKPGEELSPTDENGKVIFDIVDLCTTWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHYFNSDSFASHPNYPYS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1821
R free: 0.2275
Average B factor: 19.084
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: PEG 8000, NaCl, MES
Matthews coefficient: 2.08
Solvent content (%): 40.73
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: 2017-03-15
Human dihydrofolate reductase complexed with P39 (PDB entry 7XI7)
Macromolecule: Dihydrofolate reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.3
Sequence length: 187 residues
Sequence: MVGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1657
R free: 0.1936
Average B factor: 18.4
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 297
Crystal growth procedure: 2.85 M ammonium sulphate, 100 mM potassium phosphate
Matthews coefficient: 2.43
Solvent content (%): 49.48
Ligand: 6-hexyl-5-phenyl-pyrimidine-2,4-diamine (4RI)
Ligand formula: C16 H22 N4
Ligand molecular weight: 270.373
Ligand SMILES: CCCCCCc1c(c(nc(n1)N)N)c2ccccc2
Ligand InChI: InChI=1S/C16H22N4/c1-2-3-4-8-11-13-14(12-9-6-5-7-10-12)15(17)20-16(18)19-13/h5-7,9-10H,2-4,8,11H2,1H3,(H4,17,18,19,20)
Release date: 2022-06-29
Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1) (PDB entry 6F4P)
Macromolecule: JmjC domain-containing protein 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.47
Sequence length: 255 residues
Sequence: HHHHHHSSGVDLGTENLYFQSTVPRLHRPSLQHFREQFLVPGRPVILKGVADHWPAMQKWSLEYIQEIAGARTVPVEVGSRYTDEEWSQTLMTVNEFISKYIVNEPRDVGYLAQHQLFDQIPELKQDISIPDYASLGDGEEEEITINAWFGPQGTISPLHQDPQQNFLVQVMGRKYIRLYSPQESGALYPHDTHLLHNTSQVDVENPDLEKFPKFAKAPFLSAILSPGEILFIPVKYWHYVRALDLSFSVSFWWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1463
R free: 0.1682
Average B factor: 29
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M Bis-Tris pH 6.0, 26.4 % PEG3350, 0.002 M MnCl2, 300 nl sitting drops (sample:well, 1:2 ratio)
Matthews coefficient: 2.28
Solvent content (%): 46.16
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: 2018-04-04
Discovery of dihydroisoquinolinone derivatives as novel inhibitors of the p53-MDM2 interaction with a distinct binding mode: Hdm2 (MDM2) complexed with cpd5 (PDB entry 4ZYC)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 96 residues
Sequence: GSQIPASEQETLVRPKPELLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2203
R free: 0.2587
Average B factor: 30.121
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: reservoir: 2.2M ammonium sulphate, 0.2M KNa tartrate, protein: 10mg/ml Hdm2 in 50mM TRIS pH 8.0, 200mM NaCl, 1mM TCEP, 10% glycerol, drop: 0.2ul reservoir + 0.2ul protein
Ligand: (S)-2-(2-((2H-tetrazol-5-yl)methoxy)-4-methylphenyl)-1-(4-chlorophenyl)-6,7-diethoxy-1,2-dihydroisoquinolin-3(4H)-one (4SS)
Ligand formula: C28 H28 Cl N5 O4
Ligand molecular weight: 534.006
Ligand SMILES: CCOc1cc2c(cc1OCC)C(N(C(=O)C2)c3ccc(cc3OCc4[nH]nnn4)C)c5ccc(cc5)Cl
Ligand InChI: InChI=1S/C28H28ClN5O4/c1-4-36-24-13-19-14-27(35)34(22-11-6-17(3)12-23(22)38-16-26-30-32-33-31-26)28(18-7-9-20(29)10-8-18)21(19)15-25(24)37-5-2/h6-13,15,28H,4-5,14,16H2,1-3H3,(H,30,31,32,33)/t28-/m0/s1
Release date: 2015-07-22
Crystal structure of human MMP-7 in complex with inhibitor (PDB entry 8JUG)
Macromolecule: Matrilysin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.23
Sequence length: 175 residues
Sequence: MGYSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHQLGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYGKRSNSRKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.22122
R free: 0.23789
Average B factor: 15.598
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 10% w/v Polyethylene glycol 20000,  2% v/v 1,4-Dioxane,  100mM BICINE pH9.0
Matthews coefficient: 2.22
Solvent content (%): 44.6
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: 2023-11-01
Catalytic Improvement of an Artificial Metalloenzyme by Computational Design (PDB entry 5BRW)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MAHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGMAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSMTTPPLLESVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKLRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1388
R free: 0.1936
Average B factor: 21.966
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.9
Crystallization temperature (K): 298
Crystal growth procedure: 2.6 M ammonium sulfate, 50 mM Tris-HCl
Matthews coefficient: 2.06
Solvent content (%): 40.42
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: 2015-06-17
STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A PYRROLE-3-CARBOXYLIC ACID FRAGMENT 686 (PDB entry 6YV4)
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): 2
R work: 0.1814
R free: 0.2327
Average B factor: 45.91
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 295
Crystal growth procedure: 1.4 M AMMONIUM SULPHATE, 0.1 M CITRIC ACID, PH 4.0
Matthews coefficient: 1.98
Solvent content (%): 37.95
Ligand: 1-cyclopropyl-2,5-dimethyl-pyrrole-3-carboxylic acid (PQK)
Ligand formula: C10 H13 N O2
Ligand molecular weight: 179.216
Ligand SMILES: Cc1cc(c(n1C2CC2)C)C(=O)O
Ligand InChI: InChI=1S/C10H13NO2/c1-6-5-9(10(12)13)7(2)11(6)8-3-4-8/h5,8H,3-4H2,1-2H3,(H,12,13)
Release date: 2020-05-06
Human Erk2 with an Erk1/2 inhibitor (PDB entry 5NHF)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 381 residues
Sequence: MHHHHHHGGGENLYFQGSHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNLNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRSLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.247
R free: 0.259
Average B factor: 50.08
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 30% PegMME2K, 100mM HEPES pH 7.6, 200mM Ammonium sulfate
Matthews coefficient: 2.22
Solvent content (%): 44.68
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2017-04-19
Identification of N-(4-((1R,3S,5S)-3-amino-5-methylcyclohexyl)pyridin-3-yl)-6-(2,6-difluorophenyl)-5-fluoropicolinamide (PIM447), a Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (PIM) 1,2 and 3 Kinase Inhibitor in Clinical Trials for Hematological Malignancies (PDB entry 5DWR)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: MAHHHHHHLEVLFQGPLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1734
R free: 0.2022
Average B factor: 32.66
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 289
Crystal growth procedure: Crystallant:  0.6 to 1.0 mM Ammonium monophosphate (NH4)2HPO4, 200-350 mM sodium chloride, 0.1 M Citrate, pH 5.5, 1ul (10mg/ml) protein : 1ul crystallant
Matthews coefficient: 3.01
Solvent content (%): 59.07
Ligand: N-{4-[(1R,3S,5S)-3-amino-5-methylcyclohexyl]pyridin-3-yl}-6-(2,6-difluorophenyl)-5-fluoropyridine-2-carboxamide (5H7)
Ligand formula: C24 H23 F3 N4 O
Ligand molecular weight: 440.461
Ligand SMILES: CC1CC(CC(C1)N)c2ccncc2NC(=O)c3ccc(c(n3)c4c(cccc4F)F)F
Ligand InChI: InChI=1S/C24H23F3N4O/c1-13-9-14(11-15(28)10-13)16-7-8-29-12-21(16)31-24(32)20-6-5-19(27)23(30-20)22-17(25)3-2-4-18(22)26/h2-8,12-15H,9-11,28H2,1H3,(H,31,32)/t13-,14+,15-/m0/s1
Release date: 2015-11-11
HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Vadadustat (PDB entry 5OX6)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 252 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGEKGVRVELNKPSDSVGKDVF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.1743
R free: 0.2053
Average B factor: 54
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4000, Sitting drop (300 nl), protein-to-well ratio, 2:1
Matthews coefficient: 2.86
Solvent content (%): 56.99
Ligand: Vadadustat (A1Z)
Ligand formula: C14 H11 Cl N2 O4
Ligand molecular weight: 306.701
Ligand SMILES: c1cc(cc(c1)Cl)c2cc(c(nc2)C(=O)NCC(=O)O)O
Ligand InChI: InChI=1S/C14H11ClN2O4/c15-10-3-1-2-8(4-10)9-5-11(18)13(16-6-9)14(21)17-7-12(19)20/h1-6,18H,7H2,(H,17,21)(H,19,20)
Release date: 2017-10-18