Receptor
PDB id Resolution Class Description Source Keywords
5A07 1.9 Å EC: 2.-.-.- X-RAY STRUCTURE OF THE MANNOSYLTRANSFERASE KTR4P FROM S. CER IN COMPLEX WITH GDP SACCHAROMYCES CEREVISIAE TRANSFERASE GOLGI APPARATUS MANNOSYLTRANSFERASES GT-A MEPROTEINS
Ref.: STRUCTURE OF THE GLYCOSYLTRANSFERASE KTR4P FROM SACCHAROMYCES CEREVISIAE PLOS ONE V. 10 36239 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP B:500;
A:500;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MN B:501;
A:501;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
ACT A:1465;
B:1465;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5A07 1.9 Å EC: 2.-.-.- X-RAY STRUCTURE OF THE MANNOSYLTRANSFERASE KTR4P FROM S. CER IN COMPLEX WITH GDP SACCHAROMYCES CEREVISIAE TRANSFERASE GOLGI APPARATUS MANNOSYLTRANSFERASES GT-A MEPROTEINS
Ref.: STRUCTURE OF THE GLYCOSYLTRANSFERASE KTR4P FROM SACCHAROMYCES CEREVISIAE PLOS ONE V. 10 36239 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 5A07 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 211 families.
1 5A07 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 5A07 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDP; Similar ligands found: 153
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 GNP 0.839506 0.973684
6 G 0.828947 0.986486
7 5GP 0.828947 0.986486
8 G1R 0.82716 0.986667
9 GCP 0.82716 0.973684
10 GSP 0.817073 0.948718
11 GAV 0.797619 0.961039
12 GMV 0.792683 0.973684
13 G2P 0.77381 0.961039
14 G2R 0.770115 0.961039
15 GDP MG 0.759036 0.923077
16 GP2 0.756098 0.961039
17 GDP BEF 0.75 0.9
18 GDD 0.747253 0.961039
19 GKE 0.747253 0.961039
20 GDC 0.747253 0.961039
21 GPG 0.741573 0.961039
22 G3D 0.732558 0.986486
23 ALF 5GP 0.729412 0.888889
24 Y9Z 0.728261 0.902439
25 GTP MG 0.724138 0.923077
26 BEF GDP 0.724138 0.888889
27 G5P 0.723404 0.973684
28 GFB 0.72043 0.961039
29 GTG 0.72043 0.936709
30 GDR 0.72043 0.961039
31 G4P 0.715909 0.986486
32 GCP G 0.715909 0.935065
33 6CK 0.712766 0.936709
34 G3A 0.712766 0.973684
35 GDP ALF 0.7 0.888889
36 GDP AF3 0.7 0.888889
37 YGP 0.698925 0.901235
38 JB2 0.697917 0.961039
39 GKD 0.697917 0.961039
40 GDX 0.690722 0.973684
41 GPD 0.690722 0.925
42 GMP 0.684211 0.88
43 0O2 0.666667 0.986486
44 G G 0.659574 0.935065
45 JB3 0.656863 0.948718
46 NGD 0.650485 0.961039
47 GDP 7MG 0.636364 0.911392
48 DGI 0.636364 0.923077
49 U2G 0.634615 0.936709
50 GPX 0.634409 0.946667
51 IDP 0.632184 0.972973
52 2MD 0.632075 0.891566
53 CAG 0.62963 0.880952
54 CG2 0.622642 0.936709
55 FEG 0.619048 0.879518
56 MGD 0.614679 0.891566
57 ZGP 0.613208 0.869048
58 GH3 0.612903 0.973333
59 3GP 0.611765 0.946667
60 MD1 0.607143 0.891566
61 PGD 0.59292 0.925
62 DGT 0.591398 0.923077
63 BGO 0.588785 0.924051
64 TPG 0.582609 0.840909
65 DBG 0.582609 0.948718
66 2GP 0.574713 0.96
67 FE9 0.570175 0.776596
68 I2C FE2 CMO CMO 0.566372 0.808989
69 G A A A 0.553571 0.923077
70 MGP 0.553191 0.961039
71 U A G G 0.548673 0.935065
72 G4M 0.548387 0.880952
73 6G0 0.547368 0.961039
74 G1R G1R 0.542373 0.924051
75 P2G 0.527473 0.883117
76 PGD O 0.525 0.850575
77 ADP 0.522222 0.92
78 GGM 0.517544 0.901235
79 DG 0.516484 0.910256
80 DGP 0.516484 0.910256
81 P1G 0.516129 0.871795
82 G G U 0.509259 0.935065
83 G1G 0.508475 0.925
84 IMP 0.505495 0.959459
85 G C 0.504348 0.9
86 GPC 0.491525 0.879518
87 G7M 0.483871 0.948052
88 6AD 0.479592 0.841463
89 ATP 0.473684 0.92
90 G2Q 0.471154 0.961039
91 U G A 0.469697 0.888889
92 5FA 0.46875 0.92
93 AQP 0.46875 0.92
94 GTA 0.468468 0.936709
95 7DD 0.468085 0.906667
96 G G G RPC 0.466102 0.875
97 SGP 0.463158 0.82716
98 01G 0.462963 0.902439
99 B4P 0.457447 0.894737
100 AP5 0.457447 0.894737
101 A2D 0.456522 0.894737
102 G G G C 0.455285 0.9125
103 ACQ 0.454545 0.896104
104 5GP 5GP 0.454545 0.883117
105 ANP 0.454545 0.896104
106 A G C C 0.451613 0.911392
107 APC G U 0.45082 0.886076
108 G U34 0.449153 0.888889
109 DG DG 0.448598 0.865854
110 ITT 0.447917 0.868421
111 BA3 0.446809 0.894737
112 35G 0.444444 0.933333
113 C2E 0.444444 0.921053
114 PCG 0.444444 0.933333
115 MGO 0.441176 0.864198
116 AN2 0.4375 0.907895
117 G C C C 0.4375 0.924051
118 M33 0.43299 0.883117
119 UCG 0.429688 0.911392
120 A G U 0.42963 0.888889
121 ACP 0.428571 0.896104
122 MGQ 0.424528 0.935897
123 7DT 0.424242 0.906667
124 APR 0.424242 0.894737
125 AR6 0.424242 0.894737
126 93A 0.42268 0.833333
127 A4P 0.420168 0.869048
128 SAP 0.42 0.873418
129 AD9 0.42 0.896104
130 AGS 0.42 0.873418
131 G8D 0.42 0.875
132 CA0 0.418367 0.896104
133 ATF 0.417476 0.884615
134 AGO 0.414634 0.888889
135 NIA 0.413043 0.82716
136 MGV 0.412844 0.890244
137 TAT 0.411765 0.884615
138 A1R 0.411215 0.839506
139 ADQ 0.411215 0.871795
140 RGT 0.410714 0.909091
141 CGP 0.409836 0.86747
142 AMP 0.408602 0.893333
143 A 0.408602 0.893333
144 UP5 0.40678 0.873418
145 C2R 0.406593 0.906667
146 AMZ 0.406593 0.918919
147 JBT 0.405882 0.778947
148 A22 0.40566 0.907895
149 25L 0.405405 0.907895
150 ADX 0.40404 0.809524
151 8OD 0.401961 0.946667
152 4TC 0.4 0.851852
153 50T 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5A07; Ligand: GDP; Similar sites found: 63
This union binding pocket(no: 1) in the query (biounit: 5a07.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4L9Z COA 0.03015 0.40391 1.47493
2 2BO4 FLC 0.001346 0.46336 1.51134
3 3W54 RNB 0.01306 0.40437 1.51976
4 4JAL SAH 0.005946 0.42279 1.79641
5 3AYI FAD 0.03284 0.41957 1.84332
6 3AYI HCI 0.03381 0.41957 1.84332
7 5N2D 8J8 0.01502 0.4033 2.08333
8 5MM0 GDD 0.003937 0.44031 2.13904
9 2FFU UDP 0.003357 0.43273 2.30415
10 5AJP UDP 0.00579 0.41929 2.30415
11 4MDH NAD 0.02784 0.40208 2.39521
12 2YQS UD1 0.02802 0.40065 2.53456
13 3G6K POP 0.024 0.40899 2.92208
14 3G6K FAD 0.0344 0.40207 2.92208
15 4E5N NAD 0.03429 0.40103 3.0303
16 2CVQ NDP 0.02568 0.40511 3.0581
17 1LDN NAD 0.01402 0.42091 3.16456
18 2D7I UDP 0.0009189 0.45236 3.22581
19 4NMC FAD 0.01411 0.42736 3.22581
20 4NMC 2OP 0.01532 0.42449 3.22581
21 5DCH 1YO 0.00336 0.4378 3.64583
22 4L2I NAD 0.006044 0.45328 3.75723
23 4L2I FAD 0.004188 0.45244 3.75723
24 1VM6 NAD 0.02553 0.40135 3.94737
25 5J8O 6GZ 0.009774 0.40842 4.03226
26 1O94 AMP 0.002966 0.43737 4.16667
27 1O97 FAD 0.01859 0.43505 4.16667
28 1O97 AMP 0.01859 0.43505 4.16667
29 3CV3 UDP 0.0135 0.40367 4.4335
30 5A7Y SAH 0.009904 0.40141 4.48718
31 1NHX PEP 0.03728 0.40891 4.60829
32 1NHX FTB 0.03867 0.40891 4.60829
33 3VQ2 LP4 LP5 MYR DAO 0.03935 0.40767 4.60829
34 3BQD DAY 0.02013 0.40053 4.70588
35 1QX4 FAD 0.03008 0.40722 4.74453
36 1JV1 UD1 0.0222 0.40955 5.06912
37 5FJN FAD 0.04163 0.4072 5.29954
38 5FJN BE2 0.04462 0.4072 5.29954
39 4O8A FAD 0.01421 0.42062 5.99078
40 1TIW TFB 0.01995 0.4205 5.99078
41 1TIW FAD 0.01995 0.4205 5.99078
42 5KF6 TFB 0.0183 0.41729 5.99078
43 5KF6 FAD 0.0183 0.41729 5.99078
44 1EFV AMP 0.00818 0.45504 6.27451
45 1EFV FAD 0.009337 0.45193 6.27451
46 3DMH SAM 0.01006 0.41531 6.56168
47 3DMH GMP 0.01524 0.41531 6.56168
48 1N07 ADP 0.00748 0.41983 6.74847
49 5G3U FDA 0.04173 0.40367 6.85579
50 2BOS GLA GAL GLC NBU 0.0001365 0.43005 7.35294
51 2BOS GLA GAL GLC 0.000167 0.42691 7.35294
52 5TWJ SAM 0.01681 0.40599 8.64198
53 1HYH NAD 0.01796 0.41543 9.70874
54 1YUC EPH 0.02869 0.40013 9.80392
55 4H6Q TFB 0.02953 0.40202 10.5769
56 4H6Q FAD 0.02529 0.40156 10.5769
57 2BL9 CP6 0.02583 0.4127 15.126
58 2BL9 NDP 0.02583 0.4127 15.126
59 1QF9 C5P 0.04096 0.40125 16.4948
60 1QF9 ALF 0.04096 0.40125 16.4948
61 1QF9 ADP 0.04096 0.40125 16.4948
62 3NK7 SAM 0.007984 0.41845 16.6065
63 3QF7 ANP 0.0166 0.41596 20
Pocket No.: 2; Query (leader) PDB : 5A07; Ligand: GDP; Similar sites found: 5
This union binding pocket(no: 2) in the query (biounit: 5a07.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5M42 FMN 0.01206 0.40405 3.22581
2 4M1U MBG A2G 0.01092 0.41682 5.71429
3 1N07 FMN 0.01361 0.42275 6.74847
4 2G37 FAD 0.01671 0.4045 7.95107
5 2OQ2 A3P 0.01238 0.41411 10.3448
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