Receptor
PDB id Resolution Class Description Source Keywords
5MM0 2.3 Å EC: 7.-.-.- DOLICHYL PHOSPHATE MANNOSE SYNTHASE IN COMPLEX WITH GDP-MANN MN2+ (DONOR COMPLEX) PYROCOCCUS FURIOSUS (STRAIN ATCC 435873638 / JCM 8422 / VC1) DOLICHOL PHOSPHATE MANNOSE SYNTHASE ENZYME INTEGRAL MEMBRAPROTEIN PROTEIN GLYCOSYLATION GDP-MANNOSE MANGANESE IONCOMPLEX MEMBRANE PROTEIN
Ref.: STRUCTURAL BASIS FOR DOLICHYLPHOSPHATE MANNOSE BIOS NAT COMMUN V. 8 120 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:403;
Invalid;
none;
submit data
35.453 Cl [Cl-]
LDA A:407;
A:408;
A:406;
A:405;
A:404;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
229.402 C14 H31 N O CCCCC...
MN A:402;
Part of Protein;
none;
submit data
54.938 Mn [Mn+2...
GDD A:401;
Valid;
none;
submit data
605.341 C16 H25 N5 O16 P2 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5MM0 2.3 Å EC: 7.-.-.- DOLICHYL PHOSPHATE MANNOSE SYNTHASE IN COMPLEX WITH GDP-MANN MN2+ (DONOR COMPLEX) PYROCOCCUS FURIOSUS (STRAIN ATCC 435873638 / JCM 8422 / VC1) DOLICHOL PHOSPHATE MANNOSE SYNTHASE ENZYME INTEGRAL MEMBRAPROTEIN PROTEIN GLYCOSYLATION GDP-MANNOSE MANGANESE IONCOMPLEX MEMBRANE PROTEIN
Ref.: STRUCTURAL BASIS FOR DOLICHYLPHOSPHATE MANNOSE BIOS NAT COMMUN V. 8 120 2017
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5MLZ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5MM0 - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 families.
1 5MLZ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5MM0 - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 5MLZ - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 5MM0 - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDD; Similar ligands found: 134
No: Ligand ECFP6 Tc MDL keys Tc
1 GDD 1 1
2 GDC 1 1
3 GKE 1 1
4 GFB 0.804124 0.974359
5 GDR 0.804124 0.974359
6 6CK 0.795918 0.95
7 GDX 0.772277 0.987013
8 GP3 0.755556 0.961538
9 GDP 0.747253 0.961039
10 GKD 0.745098 1
11 JB2 0.745098 0.974359
12 GSP 0.744681 0.91358
13 GTP 0.741935 0.961039
14 GNH 0.73913 0.948718
15 G1R 0.734043 0.974026
16 JB3 0.719626 0.962025
17 GPD 0.704762 0.938272
18 GCP 0.697917 0.936709
19 G 0.692308 0.948052
20 5GP 0.692308 0.948052
21 GNP 0.690722 0.936709
22 GPG 0.683168 0.974359
23 G2R 0.673267 0.925
24 GMV 0.670103 0.936709
25 G3A 0.660377 0.961538
26 G5P 0.654206 0.961538
27 GAV 0.643564 0.925
28 Y9Z 0.641509 0.892857
29 G2P 0.64 0.925
30 GP2 0.639175 0.925
31 GTG 0.635514 0.925926
32 GDP MG 0.626263 0.888889
33 GMP 0.625 0.87013
34 GDP BEF 0.62 0.86747
35 ADQ 0.61165 0.910256
36 U2G 0.608696 0.95
37 G4M 0.604651 0.916667
38 ALF 5GP 0.60396 0.857143
39 0O2 0.603774 0.948052
40 GTP MG 0.601942 0.888889
41 BEF GDP 0.601942 0.857143
42 YGP 0.601852 0.891566
43 GCP G 0.596154 0.9
44 G4P 0.596154 0.948052
45 G3D 0.592233 0.948052
46 GDP ALF 0.584906 0.857143
47 GDP AF3 0.584906 0.857143
48 CG2 0.584746 0.95
49 G G 0.583333 0.924051
50 NGD 0.581197 0.949367
51 3GP 0.56701 0.935065
52 2MD 0.566667 0.882353
53 CAG 0.565574 0.872093
54 FEG 0.554622 0.892857
55 MGD 0.552846 0.882353
56 ZGP 0.55 0.860465
57 GDP 7MG 0.53913 0.901235
58 TPG 0.539062 0.833333
59 PGD 0.535433 0.914634
60 MD1 0.535433 0.882353
61 2GP 0.535354 0.948052
62 FE9 0.527559 0.770833
63 DBG 0.527132 0.9375
64 G A A A 0.524194 0.936709
65 U A G G 0.52 0.924051
66 G1R G1R 0.515385 0.9375
67 GH3 0.513761 0.935897
68 I2C FE2 CMO CMO 0.5 0.802198
69 DGT 0.495413 0.888889
70 IDP 0.495238 0.935065
71 GPX 0.491071 0.910256
72 DGI 0.485981 0.888889
73 G1G 0.484615 0.914634
74 BGO 0.48 0.9375
75 GPC 0.469231 0.892857
76 G C 0.46875 0.91358
77 P2G 0.466667 0.897436
78 PGD O 0.466667 0.842697
79 2GW 0.466102 0.792683
80 GUD 0.463636 0.8
81 UFM 0.463636 0.8
82 GDU 0.463636 0.8
83 MGP 0.463636 0.925
84 UPG 0.463636 0.8
85 U G A 0.461538 0.902439
86 C5G 0.460177 0.85
87 JBT 0.45977 0.810526
88 6G0 0.459459 0.925
89 G G U 0.459016 0.924051
90 P1G 0.457944 0.886076
91 GGM 0.457364 0.914634
92 DAU 0.448276 0.724138
93 IMP 0.447619 0.922078
94 GTA 0.447154 0.925926
95 DG 0.443396 0.876543
96 DGP 0.443396 0.876543
97 G U34 0.44186 0.902439
98 ADP BMA 0.435897 0.886076
99 APC G U 0.432836 0.876543
100 A2D 0.432692 0.884615
101 SAP 0.427273 0.841463
102 AGS 0.427273 0.841463
103 A G U 0.424658 0.902439
104 BA3 0.424528 0.884615
105 G G G RPC 0.424242 0.865854
106 G2Q 0.423729 0.925
107 ATP 0.422018 0.884615
108 AP5 0.420561 0.884615
109 B4P 0.420561 0.884615
110 ADP 0.420561 0.884615
111 139 0.419847 0.845238
112 AQP 0.418182 0.884615
113 APR 0.418182 0.884615
114 AR6 0.418182 0.884615
115 5FA 0.418182 0.884615
116 AN2 0.416667 0.873418
117 G7M 0.416667 0.9125
118 G G G C 0.416058 0.902439
119 AD9 0.414414 0.8625
120 UCG 0.414286 0.901235
121 A22 0.413793 0.897436
122 A G C C 0.413043 0.901235
123 SGP 0.412844 0.819277
124 ITT 0.412844 0.835443
125 ACQ 0.40708 0.8625
126 ANP 0.40708 0.8625
127 01G 0.406504 0.892857
128 1GW 0.40625 0.764706
129 DG DG 0.404959 0.879518
130 AFH 0.404762 0.855422
131 A4P 0.40458 0.882353
132 G C C C 0.401408 0.91358
133 ATF 0.4 0.851852
134 M33 0.4 0.85
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5MM0; Ligand: GDD; Similar sites found: 22
This union binding pocket(no: 1) in the query (biounit: 5mm0.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5UDS ATP 0.005188 0.43437 1.74825
2 5A07 GDP 0.003937 0.44031 2.13904
3 1JV1 UD1 0.006222 0.40279 2.13904
4 2VDF OCT 0.008003 0.40208 2.37154
5 3DXY SAM 0.0152 0.40732 2.75229
6 2BO4 FLC 0.00004075 0.48311 3.47594
7 2YQS UD1 0.00429 0.40522 3.7037
8 4YRD 3IT 0.02576 0.4124 3.89972
9 2CYB TYR 0.02516 0.41119 4.02477
10 3CU0 UDP 0.0007462 0.411 4.27046
11 3CU0 GAL GAL SO4 0.005929 0.40618 4.27046
12 1S4P GDP 0.003316 0.43933 4.88506
13 2PA4 UPG 0.0008803 0.43768 7.43034
14 5FV9 Y6W 0.0003503 0.44949 13.1016
15 5FV9 UDP 0.000432 0.44208 13.1016
16 5AJP UDP 0.000238 0.41866 13.1016
17 2FFU UDP 0.0004006 0.41735 13.1016
18 5TZJ UD1 0.0002628 0.45764 13.3152
19 2D7I UDP 0.00002824 0.43806 16.0428
20 4DEC UDP 0.007217 0.4238 27.6163
21 4DEC 3PG 0.007217 0.4238 27.6163
22 3CKJ CIT 0.0034 0.43836 27.6596
23 2G30 ALA ALA PHE 0.0004993 0.47898 50
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