Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T90167 Target Info
Target Name Polyubiquitin-C (UBC)
Synonyms ubiquitin C; HMG20
Target Type Patented-recorded Target
Gene Name UBC
UniProt ID
UBC_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Glucosamine Ligand Info
Structure Description The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier PDB:3VFK
Method X-ray diffraction Resolution 2.80 Å Mutation No [1]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGK
Residue
Distance (Å)
ARG74
3.486
Residue
Distance (Å)
GLY75
2.873
Ligand Name: CC-0651 Ligand Info
Structure Description Cdc34-ubiquitin-CC0651 complex PDB:4MDK
Method X-ray diffraction Resolution 2.61 Å Mutation No [2]
PDB Sequence
MGMQIFVKTL
8
TGKTITLEVE
18
PSDTIENVKA
28
KIQDKEGIPP
38
DQQRLIFAGK
48

QLEDGRTLSD
58
YNIQKESTLH
68
LVLRLR
Residue
Distance (Å)
GLY47
3.239
Residue
Distance (Å)
LYS48
4.742
Ligand Name: D-Alanine Ligand Info
Structure Description New strategy to analyze structures of glycopeptide-target complexes PDB:3RUL
Method X-ray diffraction Resolution 2.50 Å Mutation No [3]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGK
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DAL or .DAL2 or .DAL3 or :3DAL;style chemicals stick;color identity;select .A:77; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS77
1.329
Residue
Distance (Å)
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Ligand Name: Nicotinamide-Adenine-Dinucleotide Ligand Info
Structure Description SidE-Ubi-NAD PDB:5ZQ7
Method X-ray diffraction Resolution 2.85 Å Mutation Yes [4]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QALIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NAD or .NAD2 or .NAD3 or :3NAD;style chemicals stick;color identity;select .B:72; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG72
3.316
Residue
Distance (Å)
Ligand Name: Adenosine-5-diphosphoribose Ligand Info
Structure Description Crystal structure of Legionella effector sdeD (lpg2509) H67A in complex with ADP-ribosylated Ubiquitin PDB:6B7O
Method X-ray diffraction Resolution 1.85 Å Mutation Yes [5]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AR6 or .AR62 or .AR63 or :3AR6;style chemicals stick;color identity;select .B:42 or .B:49; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG42
1.516
Residue
Distance (Å)
GLN49
2.497
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Ligand Name: Tris(hydroxyethyl)aminomethane Ligand Info
Structure Description Crystal structure of the mouse HOIL1-L-NZF in complex with linear di-ubiquitin PDB:3B0A
Method X-ray diffraction Resolution 1.90 Å Mutation No [6]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGGMQIF
80
VKTLTGKTIT
90
LEVEPSDTIE
100

NVKAKIQDKE
110
GIPPDQQRLI
120
FAGKQLEDGR
130
TLSDYNIQKE
140
STLHLVLRLR
150

G
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TAM or .TAM2 or .TAM3 or :3TAM;style chemicals stick;color identity;select .A:118 or .A:125 or .A:148; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG118
2.875
GLN125
2.861
Residue
Distance (Å)
ARG148
2.274
Ligand Name: Ethylamine Ligand Info
Structure Description Crystal Structure of Human Otubain2 and Ubiquitin Complex PDB:4FJV
Method X-ray diffraction Resolution 2.05 Å Mutation No [7]
PDB Sequence
DVPDYAHMQI
3
FVKTLTGKTI
13
TLEVEPSDTI
23
ENVKAKIQDK
33
EGIPPDQQRL
43

IFAGKQLEDG
53
RTLSDYNIQK
63
ESTLHLVLRL
73
RG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NEH or .NEH2 or .NEH3 or :3NEH;style chemicals stick;color identity;select .B:74 or .B:75; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG74
4.710
Residue
Distance (Å)
GLY75
1.338
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Ligand Name: (2S)-2-azanyl-N-[3-(dimethylamino)propyl]-2-(3-hydroxyphenyl)ethanamide Ligand Info
Structure Description New strategy to analyze structures of glycopeptide-target complexes PDB:3RUL
Method X-ray diffraction Resolution 2.50 Å Mutation No [3]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGK
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HG7 or .HG72 or .HG73 or :3HG7;style chemicals stick;color identity;select .A:77; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS77
3.024
Residue
Distance (Å)
Ligand Name: (betaR)-3-chloro-beta-hydroxy-L-tyrosine Ligand Info
Structure Description New strategy to analyze structures of glycopeptide-target complexes PDB:3RUL
Method X-ray diffraction Resolution 2.50 Å Mutation No [3]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGK
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OMY or .OMY2 or .OMY3 or :3OMY;style chemicals stick;color identity;select .A:75 or .A:77; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY75
3.372
Residue
Distance (Å)
LYS77
3.331
Ligand Name: D-4-Hydroxyphenylglycine Ligand Info
Structure Description New strategy to analyze structures of glycopeptide-target complexes PDB:3RUL
Method X-ray diffraction Resolution 2.50 Å Mutation No [3]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGK
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GHP or .GHP2 or .GHP3 or :3GHP;style chemicals stick;color identity;select .A:77; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS77
3.429
Residue
Distance (Å)
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Ligand Name: (betaR)-beta-hydroxy-L-Tyrosine Ligand Info
Structure Description The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier PDB:3VFK
Method X-ray diffraction Resolution 2.80 Å Mutation No [1]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGK
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OMX or .OMX2 or .OMX3 or :3OMX;style chemicals stick;color identity;select .A:74 or .A:75 or .A:77; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG74
4.292
GLY75
4.087
Residue
Distance (Å)
LYS77
3.223
Ligand Name: (S)-3,5-Dihydroxyphenylglycine Ligand Info
Structure Description The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier PDB:3VFK
Method X-ray diffraction Resolution 2.80 Å Mutation No [1]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGK
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3FG or .3FG2 or .3FG3 or :33FG;style chemicals stick;color identity;select .A:77; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS77
3.247
Residue
Distance (Å)
Ligand Name: (1-Oxyl-2,2,5,5-tetramethylpyrroline-3-methyl)methanethiosulfonate Ligand Info
Structure Description Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a ligand PDB:2N2K
Method Solution NMR Resolution N.A. Mutation Yes [8]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIECVKAKI
30
QDKEGIPPDQ
40
QRLIFAGCQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGG
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MTN or .MTN2 or .MTN3 or :3MTN;style chemicals stick;color identity;select .A:20 or .A:21 or .A:22 or .A:25 or .A:47 or .A:48 or .A:49; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
SER20
3.164
ASP21
4.028
THR22
2.448
CYS25
2.019
Residue
Distance (Å)
GLY47
3.662
CYS48
2.020
GLN49
2.300
Ligand Name: 2-(2-Methoxyethoxy)ethanol Ligand Info
Structure Description Crystal structure of phosphorylated RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin PDB:7M4O
Method X-ray diffraction Resolution 2.21 Å Mutation Yes [9]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PG0 or .PG02 or .PG03 or :3PG0;style chemicals stick;color identity;select .B:74 or .B:75 or .B:76; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG74
2.694
GLY75
4.662
Residue
Distance (Å)
GLY76
3.246
Ligand Name: Methyl 4-aminobutanoate Ligand Info
Structure Description Crystal structure of UCHL3-UbVME complex PDB:1XD3
Method X-ray diffraction Resolution 1.45 Å Mutation No [10]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GVE or .GVE2 or .GVE3 or :3GVE;style chemicals stick;color identity;select .B:74 or .B:75; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG74
4.304
Residue
Distance (Å)
GLY75
1.327
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Ligand Name: Propylamine Ligand Info
Structure Description Structure of Ovarian Tumor (OTU) domain in complex with Ubiquitin PDB:3BY4
Method X-ray diffraction Resolution 1.55 Å Mutation No [11]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3CN or .3CN2 or .3CN3 or :33CN;style chemicals stick;color identity;select .B:74 or .B:75; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG74
4.586
Residue
Distance (Å)
GLY75
1.337
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Ligand Name: Selenomethionine Ligand Info
Structure Description Crystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin vinyl methyl ester PDB:4I6N
Method X-ray diffraction Resolution 1.70 Å Mutation No [12]
PDB Sequence
QIFVKTLTGK
11
TITLEVEPSD
21
TIENVKAKIQ
31
DKEGIPPDQQ
41
RLIFAGKQLE
51

DGRTLSDYNI
61
QKESTLHLVL
71
RLRG
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MSE or .MSE2 or .MSE3 or :3MSE;style chemicals stick;color identity;select .B:2 or .B:3 or .B:15 or .B:16 or .B:17 or .B:18 or .B:19 or .B:56 or .B:61 or .B:62 or .B:63; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLN2
1.328
ILE3
3.935
LEU15
3.569
GLU16
2.629
VAL17
2.723
GLU18
4.500
Residue
Distance (Å)
PRO19
3.926
LEU56
4.337
ILE61
3.950
GLN62
3.808
LYS63
3.557
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Ligand Name: 3,3-bis(sulfanyl)-~{N}-(1~{H}-1,2,3-triazol-4-ylmethyl)propanamide Ligand Info
Structure Description RCR E3 ligase E2-Ubiquitin transthiolation intermediate PDB:6T7F
Method X-ray diffraction Resolution 2.58 Å Mutation Yes [13]
PDB Sequence
QIFVKTLTGK
11
TITLEVEPSD
21
TIENVKAKIQ
31
DKEGIPPDQQ
41
RLIFAGKQLE
51

DGRTLSDYNI
61
QKESTLHLVL
71
R
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LWZ or .LWZ2 or .LWZ3 or :3LWZ;style chemicals stick;color identity;select .C:72; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG72
3.315
Residue
Distance (Å)
Ligand Name: CARBOXYMETHYLATED CYSTEINE Ligand Info
Structure Description New strategy to analyze structures of glycopeptide-target complexes PDB:3RUL
Method X-ray diffraction Resolution 2.50 Å Mutation No [3]
PDB Sequence
MQIFVKTLTG
10
KTITLEVEPS
20
DTIENVKAKI
30
QDKEGIPPDQ
40
QRLIFAGKQL
50

EDGRTLSDYN
60
IQKESTLHLV
70
LRLRGK
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CCS or .CCS2 or .CCS3 or :3CCS;style chemicals stick;color identity;select .A:74 or .A:75 or .A:77; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
ARG74
3.368
GLY75
1.323
Residue
Distance (Å)
LYS77
1.332
Click to View More Binding Site Information of This Target and Ligand Pair
References  Top
REF 1 Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach. Acta Crystallogr D Biol Crystallogr. 2013 Apr;69(Pt 4):520-33.
REF 2 E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin. Nat Chem Biol. 2014 Feb;10(2):156-163.
REF 3 A carrier protein strategy yields the structure of dalbavancin. J Am Chem Soc. 2012 Mar 14;134(10):4637-45.
REF 4 Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE. Cell. 2018 May 17;173(5):1231-1243.e16.
REF 5 Mechanism of phosphoribosyl-ubiquitination mediated by a single Legionella effector. Nature. 2018 May;557(7707):729-733.
REF 6 Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex. Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20520-5.
REF 7 The human otubain2-ubiquitin structure provides insights into the cleavage specificity of poly-ubiquitin-linkages. PLoS One. 2015 Jan 15;10(1):e0115344.
REF 8 Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition. Elife. 2015 Jun 19;4:e05767.
REF 9 Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216. Mol Cell. 2022 Feb 3;82(3):598-615.e8.
REF 10 Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate. J Biol Chem. 2005 Jan 14;280(2):1512-20.
REF 11 Structural basis for ubiquitin recognition by the Otu1 ovarian tumor domain protein. J Biol Chem. 2008 Apr 18;283(16):11038-49.
REF 12 Stabilization of an unusual salt bridge in ubiquitin by the extra C-terminal domain of the proteasome-associated deubiquitinase UCH37 as a mechanism of its exo specificity. Biochemistry. 2013 May 21;52(20):3564-78.
REF 13 Structural basis for RING-Cys-Relay E3 ligase activity and its role in axon integrity. Nat Chem Biol. 2020 Nov;16(11):1227-1236.

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