satarupa22/MacromolecularLigandDB huggingface dataset:
CDK6 in complex with Cpd13 (R)-5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl)-N-(5-(4-methylpiperazin-1-yl)pyridin-2-yl)pyrimidin-2-amine (PDB entry 6OQL)
Macromolecule: Cyclin-dependent kinase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 291 residues
Sequence: QQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVQTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDRETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLDFLHSHRVVHRDLKPQNILVTSSGQIKLADFGLARIYSFQMALTSVVVTLWYRAPEVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILDVIGLPGEEDWPRDVALPRQAFHSKSAQPIEKFVTDIDELGKDLLLKCLTFNPAKRISAYSALSHPYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.707
R work: 0.2036
R free: 0.2529
Average B factor: 123.3085
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 292
Crystal growth procedure: 13-17% PEG 3350, 80 mM NH4NO3, 100 mM MES pH 6.0
Matthews coefficient: 2.35
Solvent content (%): 47.63
Ligand: 5-fluoro-N-[5-(4-methylpiperazin-1-yl)pyridin-2-yl]-4-[(4R)-4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl]pyrimidin-2-amine (N1A)
Ligand formula: C23 H29 F N8
Ligand molecular weight: 436.528
Ligand SMILES: CC1CCCCn2c1c(cn2)c3c(cnc(n3)Nc4ccc(cn4)N5CCN(CC5)C)F
Ligand InChI: InChI=1S/C23H29FN8/c1-16-5-3-4-8-32-22(16)18(14-27-32)21-19(24)15-26-23(29-21)28-20-7-6-17(13-25-20)31-11-9-30(2)10-12-31/h6-7,13-16H,3-5,8-12H2,1-2H3,(H,25,26,28,29)/t16-/m1/s1
Release date: 2020-07-29
Crystal structure of Lys27-linked di-ubiquitin in complex with its selective interacting protein UCHL3 (PDB entry 6ISU)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase isozyme L3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 230 residues
Sequence: MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.866
R work: 0.2091
R free: 0.2644
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 18% PEG 3350 (w/v), 400 mM Ca(AC)2
Matthews coefficient: 2.27
Solvent content (%): 45.72
Release date: 2019-02-06
Monobody 12D5 bound to KRAS(G12D) (PDB entry 8F0M)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 171 residues
Sequence: GSMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.44
R work: 0.2009
R free: 0.245
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M sodium sulfate decahydrate, 20% w/v PEG3350, 0.05% w/v benzamidine hydrochloride
Matthews coefficient: 2.56
Solvent content (%): 52.02
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: 2023-07-19
Human Carbonic Anhydrase II in complex with 4-oxo-N-(4-sulfamoylphenethyl)-1,3,4,6,7,11b-hexahydro-2H-pyrazino[2,1-a]isoquinoline-2-carboxamide (PDB entry 7QZX)
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): 1.24
R work: 0.1588
R free: 0.179
Average B factor: 16.14
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Matthews coefficient: 2.11
Solvent content (%): 41.82
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: 2023-02-15
Crystal structure of Tyrosine-protein kinase receptor in complex with 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one and 5-{[2,4-dichloro-5-(pyridin-2-yl)benzene-1-carbonyl]amino}-N-(2-hydroxy-2-methylpropyl)-1-phenyl-1H-pyrazole-3-carboxamide Inhibitors (PDB entry 6D20)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 320 residues
Sequence: GSTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.1703
R free: 0.2072
Average B factor: 28.71
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 294
Crystal growth procedure: Well volume: 30.0 uL

Well Ingredients:
Polymer: 10.0 %w/v (6.0 uL of stock 50.0 %w/v) PEG 3350
Buffer: 16.0 %v/v (4.8 uL of stock 100.0 %v/v) tacsimate (pH 8.00)
Organic (non-volatile): 10.0 %v/v (3.0 uL of stock 100.0 %v/v) Ethylene glycol
Additive: 0.025 M (1.5 uL of stock 0.5 M) TCEP hydrochloride

Plate setup temperature: 13 C
Plate incubation temperature: 21 C

Drop volume from well: 0.2 uL
Drop protein volume: 0.4 uL

Protein: 6.30 mg/mL (0.17 mM)
Compound1: 1.00 mM (to aid crystallization).
Compound23 (allostric inhibitor): 1.3ul 50mM compound23 DMSO stock in 133ul protein  (0.50 mM)
Matthews coefficient: 2.29
Solvent content (%): 46.35
Ligand: 5-{[2,4-dichloro-5-(pyridin-2-yl)benzene-1-carbonyl]amino}-N-(2-hydroxy-2-methylpropyl)-1-phenyl-1H-pyrazole-3-carboxamide (FQG)
Ligand formula: C26 H23 Cl2 N5 O3
Ligand molecular weight: 524.399
Ligand SMILES: CC(C)(CNC(=O)c1cc(n(n1)c2ccccc2)NC(=O)c3cc(c(cc3Cl)Cl)c4ccccn4)O
Ligand InChI: InChI=1S/C26H23Cl2N5O3/c1-26(2,36)15-30-25(35)22-14-23(33(32-22)16-8-4-3-5-9-16)31-24(34)18-12-17(19(27)13-20(18)28)21-10-6-7-11-29-21/h3-14,36H,15H2,1-2H3,(H,30,35)(H,31,34)
Release date: 2018-05-02
SYK Kinase domain in complex with diamine inhibitor 5 (PDB entry 6ZCQ)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 299 residues
Sequence: MDTEVYESPYADPEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.32
R work: 0.189
R free: 0.244
Average B factor: 42.94
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 0.1M Na3Cit pH 6.4, 16% PEG3350, 0.2M KH2PO4
Matthews coefficient: 2.22
Solvent content (%): 44.7
Ligand: 7-[[4-[4-[[(3~{R},4~{R})-3-azanyloxan-4-yl]amino]pyrazol-1-yl]pyrimidin-2-yl]amino]-~{N},3-dimethyl-imidazo[1,5-a]pyridine-1-carboxamide (QFB)
Ligand formula: C22 H26 N10 O2
Ligand molecular weight: 462.508
Ligand SMILES: Cc1nc(c2n1ccc(c2)Nc3nccc(n3)n4cc(cn4)NC5CCOCC5N)C(=O)NC
Ligand InChI: InChI=1S/C22H26N10O2/c1-13-27-20(21(33)24-2)18-9-14(4-7-31(13)18)29-22-25-6-3-19(30-22)32-11-15(10-26-32)28-17-5-8-34-12-16(17)23/h3-4,6-7,9-11,16-17,28H,5,8,12,23H2,1-2H3,(H,24,33)(H,25,29,30)/t16-,17+/m0/s1
Release date: 2021-06-23
Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA (PDB entry 5F9F)
Macromolecule: Probable ATP-dependent RNA helicase DDX58
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 695 residues
Sequence: SVSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK
Oligomeric state: Homo 6-mer
Stoichiometry: A6
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.601
R work: 0.2028
R free: 0.2594
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 23% (w/v) PEG 3350, 0.3 M NaSCN, 100 mM MOPS (pH 7.8)
Matthews coefficient: 2.9
Solvent content (%): 57.64
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-01-13
Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors (PDB entry 4OEW)
Macromolecule: cGMP-specific 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.35
Sequence length: 347 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.44
R work: 0.2062
R free: 0.2586
Average B factor: 29.68
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 19-20%(w/v)PEG 3350, 200mM MgSO4, 100mM Tris-HCl, pH 7.5, vapor diffusion, hanging drop, temperature 293K
Matthews coefficient: 2.61
Solvent content (%): 52.82
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: 2015-04-01
Crystal structure of human TAK1 kinase domain fused with TAB1 (PDB entry 8GW3)
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: 326 residues
Sequence: AGEMIEAPSQVLNFEEIDYKEIEVEEVVGRGAFGVVCKAKWRAKDVAIKQIESESERKAFIVELRQLSRVNHPNIVKLYGACLNPVCLVMEYAEGGSLYNVLHGAEPLPYYTAAHAMSWCLQCSQGVAYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICDFGTACDIQTHMTNNKGSAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDEIGGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQHSLPPGEDGRVEPYVDFAEFYRLWSVDHGEQSVVTAP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.2213
R free: 0.2582
Average B factor: 46.87
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 289
Crystal growth procedure: 2% (v/v) Tacsimate pH7.0, 0.1M HEPES pH 7.5, 20%(w/v) PEG3350
Matthews coefficient: 3.08
Solvent content (%): 60.07
Release date: 2023-09-20
Crystal structure of thrombin in complex with a novel glucose-conjugated potent inhibitor (PDB entry 6EO8)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.20991
R free: 0.24757
Average B factor: 33.265
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG 4000, 0.1M HEPES pH7.0, 0.75M NaCl, 0.04% NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 2.58
Solvent content (%): 52.25
Ligand: N-(2-{[5-(5-chlorothiophen-2-yl)-1,2-oxazol-3-yl]methoxy}-6-[3-(beta-D-glucopyranosyloxy)propoxy]phenyl)-1-(propan-2-yl)piperidine-4-carboxamide (2FN)
Ligand formula: C32 H42 Cl N3 O10 S
Ligand molecular weight: 696.208
Ligand SMILES: CC(C)N1CCC(CC1)C(=O)Nc2c(cccc2OCc3cc(on3)c4ccc(s4)Cl)OCCCOC5C(C(C(C(O5)CO)O)O)O
Ligand InChI: InChI=1S/C32H42ClN3O10S/c1-18(2)36-11-9-19(10-12-36)31(41)34-27-21(42-13-4-14-43-32-30(40)29(39)28(38)24(16-37)45-32)5-3-6-22(27)44-17-20-15-23(46-35-20)25-7-8-26(33)47-25/h3,5-8,15,18-19,24,28-30,32,37-40H,4,9-14,16-17H2,1-2H3,(H,34,41)/t24-,28-,29+,30-,32-/m1/s1
Release date: 2017-12-13
MTH1 in complex with compound 4 (PDB entry 6US3)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 159 residues
Sequence: GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47028917623
R work: 0.1865002798
R free: 0.222219277267
Average B factor: 16.9610286914
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG 6000, 0.1M sodium acetate pH 4.0, 0.2M lithium sulfate
Matthews coefficient: 1.98
Solvent content (%): 37.93
Ligand: N-[5-(2,3-dimethylphenyl)-1,6-naphthyridin-7-yl]acetamide (8JF)
Ligand formula: C18 H17 N3 O
Ligand molecular weight: 291.347
Ligand SMILES: Cc1cccc(c1C)c2c3cccnc3cc(n2)NC(=O)C
Ligand InChI: InChI=1S/C18H17N3O/c1-11-6-4-7-14(12(11)2)18-15-8-5-9-19-16(15)10-17(21-18)20-13(3)22/h4-10H,1-3H3,(H,20,21,22)
Release date: 2020-04-01
Crystal structure of MOZ double PHD finger mutant-S210D/N235R in complex with histone H3 crotonylation at K14 (PDB entry 5B78)
Macromolecule: Histone acetyltransferase KAT6A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 131 residues
Sequence: SLPHEKDKPVAEPIPICDFCLGTKEQNREKKPEELISCADCGRSGHPSCLKFSPELTVRVKALRWQCIECKTCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRPRKKGRKLLQKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1686
R free: 0.1869
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: polyethylene glycol 4000,  lithium sulfate, Tris
Matthews coefficient: 2.48
Solvent content (%): 50.4
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-10-26
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOMB000194a (PDB entry 5QF3)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.563
R work: 0.1928
R free: 0.2162
Average B factor: 37.9912
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.35
Solvent content (%): 63.25
Ligand: 4-(4-methoxyphenyl)-6,7-dihydrothieno[3,2-c]pyridine (JLY)
Ligand formula: C14 H13 N O S
Ligand molecular weight: 243.324
Ligand SMILES: COc1ccc(cc1)C2=NCCc3c2ccs3
Ligand InChI: InChI=1S/C14H13NOS/c1-16-11-4-2-10(3-5-11)14-12-7-9-17-13(12)6-8-15-14/h2-5,7,9H,6,8H2,1H3
Release date: 2018-10-10
Human Aldose Reductase Mutant A299G/L300G in Complex with a Ligand with an IDD Structure (3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid) (PDB entry 8B3N)
Macromolecule: Aldo-keto reductase family 1 member B1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.300
Sequence length: 316 residues
Sequence: MASRILLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCGGLSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.03
R work: 0.1355
R free: 0.1543
Average B factor: 11.76
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Di-Ammoniumhydrogen citrate pH 5: 15 mg/mL hAR, 5.2 mg/mL DTT, 0.7 mg/mL NADP+, 10% (w/v) PEG 6000
Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5, 20% (w/v) PEG 6000
Soaking: 120 mM di-ammonium hydrogen citrate pH 5.0, 25% PEG 6000, saturated with ligand
Matthews coefficient: 2.17
Solvent content (%): 43.35
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: 2023-09-27
Human Cyclophilin D Complexed with an Inhibitor at room temperature (PDB entry 4ZSC)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1336
R free: 0.1628
Average B factor: 9.817
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 291
Crystal growth procedure: 30% PEG4000
Matthews coefficient: 2.1
Solvent content (%): 41.36
Ligand: ethyl N-[(4-aminobenzyl)carbamoyl]glycinate (EA4)
Ligand formula: C12 H17 N3 O3
Ligand molecular weight: 251.282
Ligand SMILES: CCOC(=O)CNC(=O)NCc1ccc(cc1)N
Ligand InChI: InChI=1S/C12H17N3O3/c1-2-18-11(16)8-15-12(17)14-7-9-3-5-10(13)6-4-9/h3-6H,2,7-8,13H2,1H3,(H2,14,15,17)
Release date: 2015-08-12
Crystal structure of the SPRY domain of SPSB2 in complex with cR7, a potent cyclic peptide inhibitor of SPSB2-iNOS interaction (PDB entry 6JWM)
Macromolecule: SPRY domain-containing SOCS box protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 209 residues
Sequence: MGDLSCPEGLEELLSAPPPDLGAQRRHGWNPKDCSENIEVKEGGLYFERRPVAQSTDGARGKRGYSRGLHAWEISWPLEQRGTHAVVGVATALAPLQTDHYAALLGSNSESWGWDIGRGKLYHQSKGPGAPQYPAGTQGEQLEVPERLLVVLDMEEGTLGYAIGGTYLGPAFRGLKGRTLYPAVSAVWGQCQVRIRYLGERGSHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.23
R work: 0.17688
R free: 0.20018
Average B factor: 9.003
Crystallization method: EVAPORATION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH6.5, 25% w/v Polyethylene glycol 3350
Matthews coefficient: 1.92
Solvent content (%): 35.91
Release date: 2020-04-22
Crystal structure of KDM5B in complex with S49365a. (PDB entry 6EIN)
Macromolecule: Lysine-specific demethylase 5B,Lysine-specific demethylase 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 481 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKINK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.196
R free: 0.225
Average B factor: 46.31
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.8M Pottassium Phosphate-dibasic, 0.8M Sodium Phosphate monobasic
Matthews coefficient: 4.4
Solvent content (%): 72.03
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 PPARgamma ligand binding dmain complexed with SB1405 in a covalent bonded form (PDB entry 5DV3)
Macromolecule: Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 287 residues
Sequence: GSHMAEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.20168
R free: 0.22995
Average B factor: 78.177
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 297
Crystal growth procedure: 2.2M sodium malonate pH 7.0
Matthews coefficient: 2.68
Solvent content (%): 54.16
Ligand: N-[2-(benzyloxy)phenyl]-3-nitrobenzamide (B05)
Ligand formula: C20 H16 N2 O4
Ligand molecular weight: 348.352
Ligand SMILES: c1ccc(cc1)COc2ccccc2NC(=O)c3cccc(c3)[N+](=O)[O-]
Ligand InChI: InChI=1S/C20H16N2O4/c23-20(16-9-6-10-17(13-16)22(24)25)21-18-11-4-5-12-19(18)26-14-15-7-2-1-3-8-15/h1-13H,14H2,(H,21,23)
Release date: 2016-09-21