satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human methionine aminopeptidase-2 complexed with (3R,4S,5S,6R)-5-methoxy-4-[(2R,3R)-2-methyl-3-(3-methyl-2-buten-1-yl)-2-oxiranyl]-1-oxaspiro[2.5]oct-6-yl N-(trans-4-aminocyclohexyl)carbamate (PDB entry 8OXG)
Macromolecule: Methionine aminopeptidase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 384 residues
Sequence: MHHHHHHENLYFQGPKVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDY
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.731
R work: 0.1811
R free: 0.215
Average B factor: 28.255
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Matthews coefficient: 2.88
Solvent content (%): 57.27
Ligand: [(1~{R},2~{S},3~{S},4~{R})-2-methoxy-4-methyl-3-[(2~{R},3~{S})-2-methyl-3-(3-methylbut-2-enyl)oxiran-2-yl]-4-oxidanyl-cyclohexyl] ~{N}-(4-azanylcyclohexyl)carbamate (W5N)
Ligand formula: C23 H40 N2 O5
Ligand molecular weight: 424.574
Ligand SMILES: CC(=CCC1C(O1)(C)C2C(C(CCC2(C)O)OC(=O)NC3CCC(CC3)N)OC)C
Ligand InChI: InChI=1S/C23H40N2O5/c1-14(2)6-11-18-23(4,30-18)20-19(28-5)17(12-13-22(20,3)27)29-21(26)25-16-9-7-15(24)8-10-16/h6,15-20,27H,7-13,24H2,1-5H3,(H,25,26)/t15-,16-,17-,18+,19-,20+,22-,23+/m1/s1
Release date: 2024-04-10
Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate P13 (PDB entry 6LJM)
Macromolecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1
Sequence length: 272 residues
Sequence: QASARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.165
R free: 0.197
Average B factor: 22.65
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 23%-27% (v/v) PEG 3350, 0.1 M MES, pH 5.5-6.0, 0.1-0.2 M NaCl
Matthews coefficient: 2.4
Solvent content (%): 48.72
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
HIF prolyl hydroxylase 2 (PHD2/EGLN1) I280V/R281L/I292V variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/FG2216) (PDB entry 5LBC)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 252 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLVLHCNGKLGSYKVNGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGEKGVRVELNKPSDSVGKDVF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.816
R work: 0.1577
R free: 0.1809
Average B factor: 39
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 6.5, 1.8 M ammonium sulphate, 5% v/v dioxane, 0.002 M MnCl2
Matthews coefficient: 2.88
Solvent content (%): 57.29
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: 2016-08-31
Ku70/80 binds to the Ku-binding motif of PAXX (PDB entry 8ASC)
Macromolecule: X-ray repair cross-complementing protein 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4
Sequence length: 544 residues
Sequence: MSGWESYYKTEGDEEAEEEQEENLEASGDYKYSGRDSLIFLVDASKAMFESQSEDELTPFDMSIQCIQSVYISKIISSDRDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKRILELDQFKGQQGQKRFQDMMGHGSDYSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRDTGIFLDLMHLKKPGGFDISLFYRDIISIAEDEDLRVHFEESSKLEDLLRKVRAKETRKRALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLPSDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEESLVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQLVFLPFADDKRKMPFTEKIMATPEQVGKMKAIVEKLRFTYRSDSFENPVLQQHFRNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSLVDEFKELVYPPDYNPEGKVTKRK
Oligomeric state: Hetero 10-mer
Stoichiometry: A4, B4, C2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.252
R free: 0.2981
Average B factor: 101.0598
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 290
Crystal growth procedure: 12% PEG- 3350; 0.1 M Bis-Tris Propane pH 8.5; 0.3 M Ammonium Sulfate
Matthews coefficient: 3.3
Solvent content (%): 62.78
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: 2023-06-21
Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418, FAD-adduct (PDB entry 7E0G)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.66
Sequence length: 665 residues
Sequence: GGSSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1935
R free: 0.2382
Average B factor: 60.134
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M imidazole/HCl (pH 7.0), 14% PEG 3350, 10% 2-methyl-2,4-pentanediol
Matthews coefficient: 3.61
Solvent content (%): 65.96
Ligand: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate (HUF)
Ligand formula: C28 H35 N9 O16 P2
Ligand molecular weight: 815.576
Ligand SMILES: Cc1cc2c(cc1C)N(C3=C(N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O)NC(=O)NC3=O)C=O
Ligand InChI: InChI=1S/C28H35N9O16P2/c1-11-3-13-14(4-12(11)2)37(10-38)19-25(33-28(45)34-26(19)44)35(13)5-15(39)20(41)16(40)6-50-54(46,47)53-55(48,49)51-7-17-21(42)22(43)27(52-17)36-9-32-18-23(29)30-8-31-24(18)36/h3-4,8-10,15-17,20-22,27,39-43H,5-7H2,1-2H3,(H,46,47)(H,48,49)(H2,29,30,31)(H2,33,34,44,45)/t15-,16+,17+,20-,21+,22+,27+/m0/s1
Release date: 2021-03-24
Crystal structure of Dot1L in complex with an inhibitor (compound 10). (PDB entry 6TEL)
Macromolecule: Histone-lysine N-methyltransferase, H3 lysine-79 specific
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 334 residues
Sequence: GPGEKLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKNPG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.19
R work: 0.185
R free: 0.212
Average B factor: 63.46
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 1.28 M K/Na tartrate
0.1 M Hepes pH 7.0
Matthews coefficient: 3.52
Solvent content (%): 65.1
Ligand: ~{N}1-[(~{S})-[2,2-bis(fluoranyl)-1,3-benzodioxol-4-yl]-(3-chloranylpyridin-2-yl)methyl]-~{N}2-(4-methoxy-6-piperazin-1-yl-1,3,5-triazin-2-yl)-4-methylsulfonyl-benzene-1,2-diamine (N4Z)
Ligand formula: C28 H27 Cl F2 N8 O5 S
Ligand molecular weight: 661.079
Ligand SMILES: COc1nc(nc(n1)N2CCNCC2)Nc3cc(ccc3NC(c4cccc5c4OC(O5)(F)F)c6c(cccn6)Cl)S(=O)(=O)C
Ligand InChI: InChI=1S/C28H27ClF2N8O5S/c1-42-27-37-25(36-26(38-27)39-13-11-32-12-14-39)35-20-15-16(45(2,40)41)8-9-19(20)34-22(23-18(29)6-4-10-33-23)17-5-3-7-21-24(17)44-28(30,31)43-21/h3-10,15,22,32,34H,11-14H2,1-2H3,(H,35,36,37,38)/t22-/m0/s1
Release date: 2019-12-11
Crystal structure of compound 4 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB (PDB entry 7Z78)
Macromolecule: Probable global transcription activator SNF2L2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4
Sequence length: 123 residues
Sequence: SMAEKLSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQKIAKEEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.32
R work: 0.187
R free: 0.21
Average B factor: 29.14
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 8% ethylene glycol, 25% PEG 6000, 0.1 M HEPES pH 8.0 and 10 mM zinc chloride
Matthews coefficient: 2.23
Solvent content (%): 44.78
Ligand: 4-bromanyl-7-cyclopentyl-9-piperidin-4-yl-benzimidazolo[1,2-a]quinazolin-5-one (IF8)
Ligand formula: C24 H25 Br N4 O
Ligand molecular weight: 465.386
Ligand SMILES: c1cc2c(c(c1)Br)C(=O)N=C3N2c4ccc(cc4N3C5CCCC5)C6CCNCC6
Ligand InChI: InChI=1S/C24H25BrN4O/c25-18-6-3-7-20-22(18)23(30)27-24-28(17-4-1-2-5-17)21-14-16(8-9-19(21)29(20)24)15-10-12-26-13-11-15/h3,6-9,14-15,17,26H,1-2,4-5,10-13H2
Release date: 2022-09-14
PIM1 in complex with Cpd4 (3-methyl-5-(pyridin-3-yl)-1H-pyrazolo[3,4-c]pyridine) (PDB entry 5DHJ)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 299 residues
Sequence: MKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSKKLAAALEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.457
R work: 0.1881
R free: 0.2497
Average B factor: 49.673
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 289
Crystal growth procedure: PEG 4000, 0.2M LiSO4, 0.1M Tris-HCl
Matthews coefficient: 3.54
Solvent content (%): 65.22
Ligand: 3-methyl-5-(pyridin-3-yl)-2H-pyrazolo[3,4-c]pyridine (5E5)
Ligand formula: C12 H10 N4
Ligand molecular weight: 210.235
Ligand SMILES: Cc1c2cc(ncc2n[nH]1)c3cccnc3
Ligand InChI: InChI=1S/C12H10N4/c1-8-10-5-11(9-3-2-4-13-6-9)14-7-12(10)16-15-8/h2-7H,1H3,(H,15,16)
Release date: 2015-10-28
Discovery of NVP-CGM097 - a highly potent and selective MDM2 inhibitor undergoing phase 1 clinical trials in p53wt tumors: Hdm2 (MDM2) complexed with NVP-CGM097 (PDB entry 4ZYF)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 96 residues
Sequence: GSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2267
R free: 0.2321
Average B factor: 24.274
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 298
Crystal growth procedure: reservoir: 2M AmSulfate, 0.1M cictric acid, pH4.5, protein: 7mg/ml Hdm2 in 50mM TRIS pH8.0, 200mM NaCl, 1mM TCEP, 10% glycerol, drop: 1ul reservoir + 1ul protein
Matthews coefficient: 2.17
Solvent content (%): 43.22
Ligand: (S)-1-(4-chlorophenyl)-7-isopropoxy-6-methoxy-2-(4-(methyl(((1r,4S)-4-(4-methyl-3-oxopiperazin-1-yl)cyclohexyl)methyl)amino)phenyl)-1,2-dihydroisoquinolin-3(4H)-one (4T4)
Ligand formula: C38 H47 Cl N4 O4
Ligand molecular weight: 659.257
Ligand SMILES: CC(C)Oc1cc2c(cc1OC)CC(=O)N(C2c3ccc(cc3)Cl)c4ccc(cc4)N(C)CC5CCC(CC5)N6CCN(C(=O)C6)C
Ligand InChI: InChI=1S/C38H47ClN4O4/c1-25(2)47-35-22-33-28(20-34(35)46-5)21-36(44)43(38(33)27-8-10-29(39)11-9-27)32-16-14-30(15-17-32)41(4)23-26-6-12-31(13-7-26)42-19-18-40(3)37(45)24-42/h8-11,14-17,20,22,25-26,31,38H,6-7,12-13,18-19,21,23-24H2,1-5H3/t26-,31-,38-/m0/s1
Release date: 2015-07-29
Crystal structure of KDM4D with tetrazolhydrazide compound 1 (PDB entry 6ETS)
Macromolecule: Lysine-specific demethylase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 341 residues
Sequence: METMKSKANCAQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.333
R work: 0.1287
R free: 0.1559
Average B factor: 18.5015
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 100mM HEPES, 180mM ammonium sulphate, 24% PEG 3350
Matthews coefficient: 2.54
Solvent content (%): 51.55
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: 2019-02-20
DHODH in complex with Ligand 26 (PDB entry 9BKO)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 367 residues
Sequence: GATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.14221
R free: 0.17007
Average B factor: 24.047
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.10 M NaAcetate pH 4.8, 2.0 M (NH4)2SO4, 30 % Glycerol
Matthews coefficient: 3.67
Ligand: FLAVIN MONONUCLEOTIDE (FMN)
Ligand formula: C17 H21 N4 O9 P
Ligand molecular weight: 456.344
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
Release date: 2024-07-03
Crystal structure of the KIX domain of CBP in complex with a MLL/c-Myb chimera (PDB entry 5SVH)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 87 residues
Sequence: GVRKGWHEHVTQDLRSHLVHKLVQAIFPTPDPAALKDRRMENLVAYAKKVEGDMYESANSRDEYYHLLAEKIYKIQKELEEKRRSRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2063
R free: 0.242
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M potassium sulfate
2.3M Ammonium sulphate
Matthews coefficient: 3.12
Solvent content (%): 60.6
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: 2018-05-09
Crystallographic solvent mapping analysis of DMSO bound to APE1 (PDB entry 6MK3)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 285 residues
Sequence: GSHMASEGPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.478
R work: 0.1908
R free: 0.2186
Average B factor: 21.43
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, pH 6.0, 200 mM sodium chloride, 18-21% PEG4000
Matthews coefficient: 2.27
Solvent content (%): 45.77
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2019-01-30
LTA4 hydrolase in complex with Compound15 (PDB entry 6END)
Macromolecule: Leukotriene A-4 hydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 613 residues
Sequence: GPGPEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPDVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.1629
R free: 0.2165
Average B factor: 24.82
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 8000, 0.1 IMIDAZOLE PH 6.8, 0.1 SODIUM ACETATE, 0.005 M YBCL3
Matthews coefficient: 2.43
Solvent content (%): 49.36
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: 2017-12-13
The Fk1 domain of FKBP51 in complex with (1S,5S,6R)-10-(benzo[d]thiazol-6-ylsulfonyl)-5-(methoxymethyl)-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one (PDB entry 7APQ)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.09
R work: 0.1812
R free: 0.2147
Average B factor: 14.79
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 36% PEG-3350, 0.2 M NH4-acetate and HEPES-NaOH pH 7.5
Matthews coefficient: 2.3
Solvent content (%): 46.48
Ligand: (1~{S},5~{S},6~{R})-10-(1,3-benzothiazol-6-ylsulfonyl)-5-(methoxymethyl)-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one (RQW)
Ligand formula: C23 H26 N4 O4 S2
Ligand molecular weight: 486.607
Ligand SMILES: COCC1CN(C(=O)C2CCCC1N2S(=O)(=O)c3ccc4c(c3)scn4)Cc5ccccn5
Ligand InChI: InChI=1S/C23H26N4O4S2/c1-31-14-16-12-26(13-17-5-2-3-10-24-17)23(28)21-7-4-6-20(16)27(21)33(29,30)18-8-9-19-22(11-18)32-15-25-19/h2-3,5,8-11,15-16,20-21H,4,6-7,12-14H2,1H3/t16-,20-,21+/m1/s1
Release date: 2021-11-10
Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue (compound 35) (PDB entry 6GQQ)
Macromolecule: Vascular endothelial growth factor receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 322 residues
Sequence: MDPDELPLDEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANAQQDENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.177
R free: 0.204
Average B factor: 30.07
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 5 % PEG 8000, 0.1 M PCTP (sodium propionate, sodium cacodylate trihydrate, bis-tris propane) pH 7.2
Matthews coefficient: 2.32
Solvent content (%): 46.96
Ligand: ~{N}-[4-(6,7-dimethoxyquinazolin-4-yl)oxyphenyl]-2-(4-propan-2-yl-1,2,3-triazol-1-yl)ethanamide (F8B)
Ligand formula: C23 H24 N6 O4
Ligand molecular weight: 448.474
Ligand SMILES: CC(C)c1cn(nn1)CC(=O)Nc2ccc(cc2)Oc3c4cc(c(cc4ncn3)OC)OC
Ligand InChI: InChI=1S/C23H24N6O4/c1-14(2)19-11-29(28-27-19)12-22(30)26-15-5-7-16(8-6-15)33-23-17-9-20(31-3)21(32-4)10-18(17)24-13-25-23/h5-11,13-14H,12H2,1-4H3,(H,26,30)
Release date: 2018-09-19
Oncogenic point mutation of RET receptor tyrosine kinase (PDB entry 6FEK)
Macromolecule: Proto-oncogene tyrosine-protein kinase receptor Ret
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 299 residues
Sequence: GPLSLSVDAFKILAAPKWEFPRKNLVLGKTLGEGEFGKVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQVNHPHVIKLYGACSQDGPLLLIVEYAKYGSLRGFLRESRKVGPGPDERALTMGDLISFAWQISQGMQYLAEMKLVHRDLAARNILVAEGRKMKISDFGLSRDVYEEDFYVKRSQGRIPVKWMAIESLFDHIYTTQSDVWSFGVLLWEIVTLGGNPYPGIPPERLFNLLKTGHRMERPDNCSEEMYRLMLQCWKQEPDKRPVFADISKDLEKMMVKRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2007
R free: 0.2441
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.4
Crystallization temperature (K): 289
Crystal growth procedure: 3.4 M sodium formate, and 0.1 M sodium acetate pH 4.4
Matthews coefficient: 2.36
Solvent content (%): 47.84
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: 2018-02-28