Receptor
PDB id Resolution Class Description Source Keywords
2GMS 1.8 Å EC: 4.-.-.- E COLI GDP-4-KETO-6-DEOXY-D-MANNOSE-3-DEHYDRATASE WITH BOUND PLP ESCHERICHIA COLI COLITOSE 0-ANTIGEN ASPARTATE AMINOTRANSFERASE PLP DEOXYSTRANSFERASE
Ref.: THE STRUCTURE OF GDP-4-KETO-6-DEOXY-D-MANNOSE-3-DEH A UNIQUE COENZYME B6-DEPENDENT ENZYME. PROTEIN SCI. V. 15 2093 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:403;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
P0P A:400;
B:401;
 Valid;
Valid;
 none;
none;
 submit data
265.157 C8 H12 N O7 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3B8X 1.7 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXYMANNOSE-3-DEHYDRATASE H188N MUTANT WITH BOUND GDP-PEROSAMINE ESCHERICHIA COLI ASPARTATE AMINOTRANSFERASE COLITOSE PEROSAMINE O-ANTIGENPYRIDOXAL PHOSPHATE TRANSFERASE
Ref.: GDP-4-KETO-6-DEOXY-D-MANNOSE 3-DEHYDRATASE, ACCOMMO SUGAR SUBSTRATE IN THE ACTIVE SITE. J.BIOL.CHEM. V. 283 4295 2008
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 62 families.
1 3GR9 - AKG C5 H6 O5 C(CC(=O)O)....
2 2GMU - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
3 3B8X - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
4 2GMS - P0P C8 H12 N O7 P Cc1c(c(c(c....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 59 families.
1 3GR9 - AKG C5 H6 O5 C(CC(=O)O)....
2 2GMU - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
3 3B8X - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
4 2GMS - P0P C8 H12 N O7 P Cc1c(c(c(c....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 47 families.
1 3GR9 - AKG C5 H6 O5 C(CC(=O)O)....
2 2GMU - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
3 3B8X - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
4 2GMS - P0P C8 H12 N O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: P0P; Similar ligands found: 50
No: Ligand ECFP6 Tc MDL keys Tc
1 P0P 1 1
2 PLR 0.557692 0.895833
3 PLP 0.527273 0.916667
4 PZP 0.517857 0.88
5 PXP 0.517857 0.9
6 PMP 0.508772 0.8
7 GT1 0.5 0.830189
8 EPC 0.461538 0.826923
9 IN5 0.454545 0.758621
10 PLG 0.454545 0.75
11 2BK 0.442857 0.793103
12 2BO 0.442857 0.793103
13 TLP 0.442857 0.793103
14 AN7 0.439394 0.88
15 PDA 0.434783 0.762712
16 PDD 0.434783 0.762712
17 PP3 0.434783 0.762712
18 F0G 0.434783 0.830189
19 EXT 0.432836 0.767857
20 FOO 0.432836 0.814815
21 OJQ 0.430556 0.625
22 33P 0.428571 0.745763
23 KOU 0.428571 0.836364
24 PL6 0.424658 0.785714
25 PLS 0.422535 0.779661
26 4LM 0.42029 0.785714
27 0JO 0.42029 0.77193
28 FEJ 0.418919 0.851852
29 PFM 0.418919 0.77193
30 CBA 0.418919 0.754098
31 C6P 0.416667 0.75
32 PPD 0.416667 0.75
33 MPM 0.414286 0.781818
34 P1T 0.414286 0.714286
35 PY5 0.410959 0.703125
36 CKT 0.408451 0.762712
37 IK2 0.408451 0.714286
38 FEV 0.408451 0.77193
39 6DF 0.405405 0.811321
40 P3D 0.402778 0.704918
41 PMH 0.402778 0.642857
42 HCP 0.402778 0.741379
43 5PA 0.402778 0.714286
44 EVM 0.402778 0.821429
45 N5F 0.402597 0.714286
46 7XF 0.4 0.725806
47 Z98 0.4 0.721311
48 PGU 0.4 0.725806
49 PDG 0.4 0.725806
50 ILP 0.4 0.737705
Similar Ligands (3D)
Ligand no: 1; Ligand: P0P; Similar ligands found: 185
No: Ligand Similarity coefficient
1 PLP PMP 0.9412
2 X04 0.9399
3 N2M 0.9239
4 NPL 0.9181
5 BG6 0.9179
6 L21 0.9162
7 G6P 0.9147
8 OSB 0.9140
9 4R1 0.9138
10 GLP 0.9111
11 GI1 0.9045
12 M6D 0.9040
13 V1T 0.9039
14 QMS 0.9034
15 M3Q 0.9012
16 S8A 0.9002
17 1QV 0.9001
18 M6P 0.8997
19 68A 0.8997
20 2VQ 0.8994
21 2GQ 0.8986
22 GI3 0.8983
23 2K8 0.8981
24 EUE 0.8976
25 SG2 0.8965
26 HBI 0.8964
27 HHS 0.8958
28 LIP 0.8953
29 790 0.8953
30 5WN 0.8950
31 ZEC 0.8943
32 A6P 0.8935
33 4KR 0.8933
34 6HP 0.8926
35 F5C 0.8921
36 GZV 0.8920
37 NBV 0.8917
38 IPD 0.8912
39 5TY 0.8912
40 STT 0.8899
41 NAG 0.8899
42 MP5 0.8899
43 AVO 0.8883
44 H4B 0.8878
45 O2Y 0.8874
46 IOS 0.8869
47 AKD 0.8868
48 SG6 0.8864
49 AJD 0.8861
50 CPW 0.8855
51 3LJ 0.8853
52 H2B 0.8845
53 LP8 0.8845
54 BGP 0.8845
55 B61 0.8845
56 BIO 0.8834
57 DNA 0.8832
58 GI4 0.8830
59 EV2 0.8828
60 5V7 0.8823
61 CFA 0.8822
62 3Y7 0.8821
63 IAC 0.8820
64 BY5 0.8818
65 CTE 0.8816
66 5WM 0.8809
67 THA 0.8809
68 DY5 0.8806
69 0J5 0.8805
70 3JM 0.8805
71 F1X 0.8805
72 5OO 0.8804
73 I4D 0.8801
74 RVE 0.8801
75 SBK 0.8799
76 I59 0.8790
77 4KL 0.8783
78 QIF 0.8781
79 7AP 0.8781
80 IOP 0.8780
81 TNX 0.8762
82 XFE 0.8757
83 657 0.8756
84 MUR 0.8752
85 TOM 0.8746
86 KED 0.8746
87 D6G 0.8745
88 GC2 0.8740
89 T6Z 0.8736
90 5GT 0.8736
91 KYA 0.8733
92 CX4 0.8732
93 X0T 0.8732
94 AC2 0.8730
95 ZON 0.8725
96 54X 0.8720
97 M5H 0.8718
98 89J 0.8717
99 APS 0.8715
100 FWD 0.8714
101 M02 0.8713
102 QUB 0.8713
103 4MX 0.8712
104 YO5 0.8712
105 NQH 0.8711
106 TRP 0.8708
107 0FR 0.8708
108 9F8 0.8706
109 CHQ 0.8705
110 67Y 0.8705
111 F52 0.8703
112 S0G 0.8703
113 3RI 0.8697
114 878 0.8697
115 MD6 0.8694
116 GDL 0.8691
117 6DP 0.8684
118 4AB 0.8681
119 3GC 0.8680
120 96Z 0.8679
121 BQ2 0.8679
122 9KZ 0.8678
123 PVQ 0.8676
124 TU0 0.8672
125 NBG 0.8671
126 96R 0.8670
127 7L4 0.8668
128 F06 0.8667
129 BA5 0.8664
130 B56 0.8661
131 CC5 0.8659
132 ARP 0.8659
133 9BF 0.8655
134 MQG 0.8654
135 3IL 0.8653
136 RGG 0.8652
137 PVK 0.8651
138 9E3 0.8649
139 3B4 0.8648
140 BNX 0.8645
141 ABF 0.8643
142 PW1 0.8641
143 HSX 0.8637
144 KF5 0.8635
145 DTR 0.8634
146 57O 0.8627
147 L07 0.8623
148 CWD 0.8616
149 KYN 0.8616
150 IBM 0.8616
151 A4V 0.8612
152 BWD 0.8608
153 AMR 0.8607
154 FC3 0.8599
155 3WN 0.8599
156 3WO 0.8599
157 ANF 0.8597
158 ALX 0.8597
159 OUB 0.8594
160 P4L 0.8592
161 49N 0.8592
162 MFR 0.8588
163 NFM 0.8588
164 3JL 0.8585
165 TB8 0.8583
166 IQZ 0.8581
167 FUZ 0.8580
168 TSR 0.8579
169 5WU 0.8577
170 SYE 0.8577
171 EUH 0.8575
172 AA 0.8575
173 ZEZ 0.8568
174 3M8 0.8562
175 CGW 0.8562
176 NPA 0.8561
177 56N 0.8558
178 IWD 0.8556
179 CR1 0.8555
180 7M2 0.8552
181 GFP 0.8538
182 ONZ 0.8526
183 30G 0.8522
184 CP7 0.8512
185 GC3 0.8505
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3B8X; Ligand: G4M; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 3b8x.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 5K8B PDG 35.641
2 3DR4 G4M 47.4359
Pocket No.: 2; Query (leader) PDB : 3B8X; Ligand: G4M; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 3b8x.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 5K8B PDG 35.641
2 3DR4 G4M 47.4359
APoc FAQ
Feedback