Receptor
PDB id Resolution Class Description Source Keywords
2GEK 2.4 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF PHOSPHATIDYLINOSITOL MANNOSYLTRANSFERAS FROM MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH GDP MYCOBACTERIUM SMEGMATIS GT4 GLYCOSYLTRANSFERASE MANNOSYLTRANSFERASE ROSSMANN FOLDCOMPLEX TRANSFERASE
Ref.: MOLECULAR RECOGNITION AND INTERFACIAL CATALYSIS BY ESSENTIAL PHOSPHATIDYLINOSITOL MANNOSYLTRANSFERASE MYCOBACTERIA. J.BIOL.CHEM. V. 282 20705 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GDP A:2567;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2GEK 2.4 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF PHOSPHATIDYLINOSITOL MANNOSYLTRANSFERAS FROM MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH GDP MYCOBACTERIUM SMEGMATIS GT4 GLYCOSYLTRANSFERASE MANNOSYLTRANSFERASE ROSSMANN FOLDCOMPLEX TRANSFERASE
Ref.: MOLECULAR RECOGNITION AND INTERFACIAL CATALYSIS BY ESSENTIAL PHOSPHATIDYLINOSITOL MANNOSYLTRANSFERASE MYCOBACTERIA. J.BIOL.CHEM. V. 282 20705 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 2GEK - 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 2GEK - 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 2GEK - 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 : 2GEK; Ligand: GDP; Similar sites found: 50
This union binding pocket(no: 1) in the query (biounit: 2gek.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4AUA 4AU 0.004037 0.4222 1.30293
2 3CV3 UDP 0.00001623 0.49524 1.72414
3 4F97 GDP 0.001706 0.43974 1.97044
4 3BEO UDP 0.001601 0.42083 2.13333
5 3G6M CFF 0.018 0.40206 2.21675
6 4U63 FAD 0.0213 0.40426 2.46305
7 3PTG 932 0.002368 0.4382 2.47934
8 4X1T UDP 0.005427 0.41621 2.69608
9 1RZU ADP 0.001136 0.44803 2.70936
10 4GYW UDP 0.01078 0.42385 2.70936
11 5BNW 12V 0.0125 0.4218 2.70936
12 2Z48 NGA 0.0104 0.41095 2.70936
13 5LWV UDP 0.01817 0.40766 2.70936
14 1EXF GLY 0.000434 0.50272 2.89256
15 4NES UDP 0.001417 0.41612 2.94118
16 5UIU 8CG 0.02311 0.40616 3.40557
17 1E7S NAP 0.02596 0.40476 3.42679
18 5X8G S0N 0.01027 0.44038 3.50515
19 3C1O NAP 0.01888 0.40273 3.73832
20 5ENZ UDP 0.002419 0.40681 3.8961
21 4JIQ FMN 0.02003 0.4029 4.24403
22 3MVH WFE 0.02666 0.40068 4.38596
23 3CH6 NAP 0.03589 0.41918 4.54545
24 1BZL FAD 0.04565 0.42707 4.6798
25 5HVJ ANP 0.01764 0.40056 4.7619
26 5TWJ SAM 0.01189 0.4094 4.93827
27 3HBN UDP 0.0001259 0.49472 5.41872
28 3UYK 0CX 0.02388 0.40981 5.42636
29 2WTX UDP 0.000008314 0.41179 5.66502
30 2WTX VDO 0.00000893 0.40686 5.66502
31 4IP7 FLC 0.01465 0.40435 5.66502
32 4YLL 4E3 0.01092 0.41117 5.81717
33 1RYA GDP 0.009563 0.41857 6.25
34 4L2I NAD 0.04514 0.40361 6.46388
35 4MO2 FDA 0.03293 0.40467 6.52174
36 1U59 STU 0.003088 0.40289 6.96864
37 4X7R UDP 0.00003703 0.47529 8.86699
38 4X7R 3YW 0.0002683 0.40361 8.86699
39 4CNG SAH 0.0115 0.41608 9.41177
40 3IES M24 0.02774 0.40547 9.85222
41 1F6D UDP 0.001792 0.43874 10.3723
42 1Y9Q MED 0.01613 0.4069 15.625
43 3RHZ UDP 0.0006007 0.429 15.9292
44 4PQG UDP 0.00009823 0.4502 16.0099
45 2IW1 U2F 0.0002528 0.40678 16.5775
46 4YZC STU 0.017 0.41728 17.5309
47 4XSU UDP 0.00001619 0.55293 23.7113
48 4XSU GLC 0.00001619 0.55293 23.7113
49 3OKP GDD 0.000000445 0.58395 30.7107
50 3OKA GDD 0.0000003205 0.59393 33.3333
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