Receptor
PDB id Resolution Class Description Source Keywords
1RYA 1.3 Å EC: 3.6.1.- CRYSTAL STRUCTURE OF THE E. COLI GDP-MANNOSE MANNOSYL HYDROLASE IN COMPLEX WITH GDP AND MG ESCHERICHIA COLI GDP-MANNOSE MANNOSE GDP-GLUCOSE NUDIX NUDIX MG-COMPLEX HYDROLASE
Ref.: STRUCTURE AND MECHANISM OF GDP-MANNOSE GLYCOSYL HYDROLASE, A NUDIX ENZYME THAT CLEAVES AT CARBON INSTEAD OF PHOSPHORUS. STRUCTURE V. 12 927 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL B:1003;
Invalid;
none;
submit data
35.453 Cl [Cl-]
GDP A:770;
B:771;
Valid;
Valid;
none;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
MG A:1001;
B:1002;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
TRS A:870;
B:871;
Invalid;
Invalid;
none;
none;
submit data
122.143 C4 H12 N O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1RYA 1.3 Å EC: 3.6.1.- CRYSTAL STRUCTURE OF THE E. COLI GDP-MANNOSE MANNOSYL HYDROLASE IN COMPLEX WITH GDP AND MG ESCHERICHIA COLI GDP-MANNOSE MANNOSE GDP-GLUCOSE NUDIX NUDIX MG-COMPLEX HYDROLASE
Ref.: STRUCTURE AND MECHANISM OF GDP-MANNOSE GLYCOSYL HYDROLASE, A NUDIX ENZYME THAT CLEAVES AT CARBON INSTEAD OF PHOSPHORUS. STRUCTURE V. 12 927 2004
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 1RYA - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 2GT4 - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 2I8U - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 2I8T - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
3 1RYA - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 2GT4 - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 2I8U - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 2I8T - GDD C16 H25 N5 O16 P2 c1nc2c(n1[....
3 1RYA - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 2GT4 - GDD C16 H25 N5 O16 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 : 1RYA; Ligand: GDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1rya.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1RYA; Ligand: GDP; Similar sites found: 86
This union binding pocket(no: 2) in the query (biounit: 1rya.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4QM9 CYS 0.005588 0.44549 None
2 2DTJ THR 0.005434 0.43492 None
3 2UVO NDG 0.02617 0.41398 None
4 1SL6 GAL NDG FUC 0.02105 0.40479 None
5 3AB4 THR 0.006878 0.43439 1.25
6 5FPE 3TR 0.003583 0.45068 1.875
7 2OUA AES 0.03124 0.40796 1.875
8 4A3X LAT 0.006271 0.45529 2.5
9 1UYY BGC BGC 0.03495 0.4021 3.05344
10 1O72 PC 0.006764 0.44987 3.125
11 3FW3 GLC 0.01165 0.42853 3.125
12 3AVS OGA 0.02857 0.40269 3.125
13 1W8S FBP 0.01735 0.40235 3.125
14 2HJR CIT 0.03062 0.40114 3.125
15 1NFS DED 0.0004706 0.47165 3.75
16 5J6Y GLC 0.00392 0.45501 3.75
17 5J6Y BGC 0.00392 0.45501 3.75
18 2ET1 GLV 0.01309 0.42615 3.75
19 2WBV SIA 0.01487 0.4255 3.75
20 5UI2 SUC 0.01599 0.4202 3.75
21 4YRD 3IT 0.02104 0.4185 3.75
22 2D24 XYS XYS 0.03427 0.41354 3.75
23 3OKP GDD 0.01593 0.40412 3.75
24 2EPN NGT 0.03222 0.40404 3.75
25 4JOB TLA 0.01711 0.40264 3.75
26 4NS0 PIO 0.007603 0.43429 3.7594
27 5FUI APY 0.003373 0.44188 3.78788
28 5AIG VPR 0.0147 0.41336 4
29 1BC5 ACE ASN TRP GLU THR PHE 0.01965 0.41105 4.375
30 4HPP GLU 0.02904 0.4047 4.375
31 4DSU BZI 0.03499 0.40359 4.375
32 3AJ6 NGA 0.04421 0.40044 4.375
33 1KNM LAT 0.02991 0.40865 4.61538
34 1JN2 SFP 0.03284 0.42274 5
35 2QX0 PH2 0.0298 0.40473 5.03145
36 4YVN EBS 0.008423 0.43682 5.625
37 4M26 AKG 0.03717 0.40136 5.625
38 2Z49 AMG 0.004424 0.46135 6.25
39 2Z48 NGA 0.006798 0.44488 6.25
40 2Z48 A2G 0.0122 0.43238 6.25
41 3G5N PB2 0.01305 0.42666 6.25
42 2GEK GDP 0.009563 0.41857 6.25
43 5LY1 PPI 0.01341 0.40747 6.25
44 1JZN BGC GAL 0.005246 0.45905 6.66667
45 2ICK DMA 0.005373 0.43074 6.875
46 1EPB REA 0.00976 0.41059 6.875
47 4KBA 1QM 0.02226 0.40827 6.875
48 1JPA ANP 0.02188 0.40719 6.875
49 3NBC LAT 0.02303 0.41514 7.43243
50 5MST FUM 0.01273 0.42072 7.5
51 4GLW NMN 0.01934 0.41211 7.5
52 3CM2 X23 0.02464 0.41014 7.69231
53 5M6M 7H8 0.01791 0.41312 7.87402
54 1QVJ RP5 0.002493 0.46604 8.125
55 4LO2 GAL BGC 0.01039 0.44425 8.125
56 4OUJ LBT 0.01106 0.44267 8.125
57 1C5C TK4 0.01053 0.42975 8.125
58 1VBH PEP 0.0195 0.41621 8.125
59 5M6N 7H9 0.03582 0.40307 8.47458
60 3UW5 MAA CHG PRO 0DQ 0.03298 0.40501 8.62069
61 4COV GLA GAL 0.02361 0.41715 8.75
62 4K55 H6P 0.03075 0.40435 8.75
63 1Z6K OAA 0.02914 0.4026 8.75
64 5J8O 6GZ 0.009325 0.41151 8.87097
65 4YEE 4CQ 0.03078 0.40676 8.88889
66 1Y7P RIP 0.02834 0.40593 9.375
67 1X9I G6Q 0.02111 0.40179 9.375
68 3IWD M2T 0.01572 0.42044 10.2941
69 4ZGR NGA GAL 0.04125 0.40031 10.625
70 2VDF OCT 0.002279 0.4662 11.25
71 3NZ1 3NY 0.01639 0.42313 11.25
72 5FJJ MAN 0.02307 0.40865 11.25
73 2CJU PHX 0.02157 0.41114 11.5044
74 4JEJ 1GP 0.01371 0.41095 12.5
75 4CJN QNZ 0.03356 0.40511 12.5
76 4OCT AKG 0.02676 0.40033 16.25
77 5DEQ ARA 0.001442 0.46897 16.875
78 3GZ8 APR 0.00003575 0.46187 17.5
79 2WZ5 MET 0.006104 0.42579 18.3007
80 2FVV IHP 0.005295 0.44018 18.75
81 5HZX 2GE 0.004481 0.43908 19.375
82 1VBO MAN 0.03172 0.40157 20.1342
83 3H0L ADP 0.01491 0.41721 21.25
84 5ISY NAD 0.002185 0.4497 23.75
85 5GG9 8GT 0.004319 0.42704 25.625
86 5LPG 71V 0.0007303 0.484 35.3659
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