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Receptor
PDB id Resolution Class Description Source Keywords
4PTN 1.99 Å EC: 4.1.2.- CRYSTAL STRUCTURE OF YAGE, A KDG ALDOLASE PROTEIN IN COMPLEX MAGNESIUM CATION COORDINATED L-GLYCERALDEHYDE ESCHERICHIA COLI TIM BARREL NAL SUPERFAMILY ALDOLASE CLASS I METAL COORDINLYASE STEREOSPECIFICITY
Ref.: CRYSTAL STRUCTURE OF YAGE, A PUTATIVE DHDPS-LIKE PR FROM ESCHERICHIA COLI K12. PROTEINS V. 71 2102 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:404;
C:405;
D:404;
B:407;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
GXV D:403;
B:406;
C:404;
A:403;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
90.078 C3 H6 O3 C(C(C...
EDO D:402;
A:402;
C:401;
D:401;
A:401;
B:401;
C:403;
B:403;
B:402;
C:402;
B:404;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
PYR B:408;
D:405;
Valid;
Valid;
none;
none;
submit data
88.062 C3 H4 O3 CC(=O...
GOL B:405;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4PTN 1.99 Å EC: 4.1.2.- CRYSTAL STRUCTURE OF YAGE, A KDG ALDOLASE PROTEIN IN COMPLEX MAGNESIUM CATION COORDINATED L-GLYCERALDEHYDE ESCHERICHIA COLI TIM BARREL NAL SUPERFAMILY ALDOLASE CLASS I METAL COORDINLYASE STEREOSPECIFICITY
Ref.: CRYSTAL STRUCTURE OF YAGE, A PUTATIVE DHDPS-LIKE PR FROM ESCHERICHIA COLI K12. PROTEINS V. 71 2102 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4PTN - GXV C3 H6 O3 C(C(C=O)O)....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4PTN - GXV C3 H6 O3 C(C(C=O)O)....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4PTN - GXV C3 H6 O3 C(C(C=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GXV; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 GXV 1 1
2 3GR 1 1
3 RB5 0.4 0.809524
4 XLS 0.4 0.809524
5 ROR 0.4 0.809524
Ligand no: 2; Ligand: PYR; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 PYR 1 1
2 ACY 0.636364 0.636364
3 OXD 0.545455 0.642857
4 F50 0.428571 0.6
5 2KT 0.411765 0.733333
6 AAE 0.411765 0.625
7 KIV 0.411765 0.785714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4PTN; Ligand: GXV; Similar sites found with APoc: 173
This union binding pocket(no: 1) in the query (biounit: 4ptn.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 3ABI NAD 1.45773
2 1NZY BCA 1.48699
3 2RC5 FAD 1.59236
4 1ZOS MTM 1.73913
5 2I6A 5I5 1.73913
6 4ZH7 FUC GAL NAG GAL FUC 1.74927
7 1X7D NAD 1.74927
8 1GQ2 NAP 1.8018
9 5A5W GUO 1.97628
10 3H22 B53 2.0202
11 1GPM CIT 2.04082
12 1XLI GLT 2.04082
13 2CVZ NDP 2.07612
14 3EJW PAV 2.22222
15 4CNE SAH 2.24719
16 2DFV NAD 2.33236
17 1YP4 ADP 2.33236
18 3GFB NAD 2.33236
19 1GZ4 ATP 2.33236
20 5VEQ PMP 2.33236
21 1R6W 164 2.48447
22 5M42 FMN 2.50896
23 4K26 SFF 2.53623
24 1QX4 FAD 2.55474
25 3F3E LEU 2.62391
26 3HAZ FAD 2.62391
27 1YKF NAP 2.62391
28 4B4D FAD 2.67176
29 1KPG SAH 2.78746
30 1KPH SAH 2.78746
31 4BMX ADE 2.78884
32 2I7C AAT 2.82686
33 4D3F NAP 2.90323
34 2I80 G1L 2.91545
35 1O0S NAI 2.91545
36 2D2I NAP 2.91545
37 3OTX AP5 2.91545
38 3VZ3 NAP 2.91545
39 4FFS BIG 2.92887
40 4JWJ SAH 2.9703
41 6BQ6 TER 3.02115
42 3H4V NAP 3.125
43 1TIW FAD 3.207
44 1TIW TFB 3.207
45 4I6G FAD 3.207
46 1QZZ SAM 3.207
47 4D57 ARG AMP 3.4904
48 1JGT APC 3.49854
49 1JGT CMA 3.49854
50 3GMB FAD 3.49854
51 2V68 CAP 3.57143
52 2V63 CAP 3.57143
53 2VDH CAP 3.57143
54 2V6A CAP 3.57143
55 2V67 CAP 3.57143
56 1IR2 CAP 3.57143
57 1GK8 CAP 3.57143
58 1AOE GW3 3.64583
59 1AOE NDP 3.64583
60 1UZD CAP 3.73134
61 5E3Q SCA 3.79009
62 2VVL FAD 3.79009
63 2C6Q NDP 3.79009
64 1K3T BRZ 3.79009
65 2C6Q IMP 3.79009
66 5U5G NAP 3.79009
67 4I8P NAD 3.79009
68 6A0J GLC GLC GLC GLC 3.79009
69 6GIU L69 3.97112
70 2ABS ACP 4.08163
71 2Y5S 78H 4.08163
72 4PLT OXM 4.22961
73 5ZAI COA 4.2471
74 5N9Z CAP 4.31655
75 5OYA CAP 4.31655
76 4PJT 2YQ 4.32432
77 3NTY 5P3 4.33437
78 4NMC 2OP 4.37318
79 4NMC FAD 4.37318
80 1REO FAD 4.37318
81 5A7Y SAH 4.48718
82 4UBT 3G6 4.66472
83 2XXP DSL 4.66472
84 1XAJ NAD 4.66472
85 1XAJ CRB 4.66472
86 1J3I NDP 4.87805
87 3O7B SAH 4.91803
88 1ADO 13P 4.95627
89 3KJS NAP 4.95627
90 3KJS DQ1 4.95627
91 5UMY TNN 5
92 6EMU SAM 5.07614
93 2IVN ANP 5.15152
94 4O8A FAD 5.24781
95 4I3V NAD 5.24781
96 3BBD SAH 5.53936
97 3GD4 FAD 5.53936
98 4KM2 ATR 5.58659
99 4FC7 NAP 5.77617
100 4FC7 COA 5.77617
101 1NVM NAD 5.7971
102 6IS0 SAH 5.8309
103 1XIM XYL 5.8309
104 1CL2 PPG 5.8309
105 2IVD FAD 5.8309
106 3CRZ FAD 5.83658
107 3CRZ NAP 5.83658
108 3OII SAH 5.92885
109 4OR7 NAP 6.06061
110 5UKL SIX 6.12245
111 1TJY PAV 6.12245
112 5TWJ SAM 6.17284
113 5YRV 5AD 6.5
114 1V2X SAM 6.70103
115 1W8S FBP 6.84411
116 4JAL SAH 7.18563
117 5F7Y GLC GAL NAG GAL FUC A2G 7.28863
118 1TPY SAH 7.31707
119 3E85 BSU 7.59494
120 2G37 FAD 7.64526
121 1P9P SAH 7.66284
122 4MCC 21X 7.72358
123 1T90 NAD 7.87172
124 1R27 MGD 7.87172
125 1EKO I84 7.93651
126 1EKO NAP 7.93651
127 5KF6 FAD 8.16327
128 5KF6 TFB 8.16327
129 4IF4 BEF 8.17308
130 6CDO ALA VAL GLY ILE GLY ALA VAL PHE 8.21918
131 5TS5 FAD 8.45481
132 1M5W DXP 8.64198
133 1EYE PMM 8.92857
134 1MXH DHF 9.42029
135 1MXH NAP 9.42029
136 4HPH SUC 9.62099
137 1EC9 XYH 9.62099
138 5FWA J7C 9.91254
139 3EYA FAD 10.3825
140 3KDN CAP 10.4956
141 4POO SAM 10.5
142 2QUN FUD 11.0345
143 5XSS XYP 11.0759
144 4H6Q TFB 11.2179
145 4H6Q FAD 11.2179
146 5XSJ XYP 11.4379
147 6CLV 6MB 11.6838
148 4N65 AQN 11.7925
149 4N65 FMN 11.7925
150 3VKC FPQ 12.2378
151 5O2Z FLC 12.605
152 5M7P ADP 12.828
153 1RBL CAP 12.844
154 5SVV FMN 13.1387
155 2GK6 ADP 14.2857
156 4II2 ATP 14.4578
157 1FDJ 2FP 14.8688
158 1FDJ 13P 14.8688
159 1MXI SAH 15
160 2PWG CTS 16.9096
161 3NK7 SAM 16.9675
162 4IXH IMP 17.2012
163 2TPS TPS 20.7048
164 1UZH CAP 21.3115
165 1WDD CAP 28.9062
166 3FGZ BEF 31.25
167 4IMG NGF 36.8601
168 4BWL MN9 38.1924
169 2WPB ZZI 38.484
170 1F74 NAY 40.6143
171 3I7S PYR 40.7534
172 1W3T 3GR 41.1079
173 5KZD RCJ 44.7099
Pocket No.: 2; Query (leader) PDB : 4PTN; Ligand: GXV; Similar sites found with APoc: 38
This union binding pocket(no: 2) in the query (biounit: 4ptn.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1JXZ BCA 1.48699
2 4W6Z 8ID 2.04082
3 6MJF SAH 2.04082
4 2GCG NDP 2.12121
5 2Q4W FAD 2.33236
6 3CH6 311 2.44755
7 3CH6 NAP 2.44755
8 4GE6 B26 2.54777
9 1ECE BGC BGC BGC BGC 2.62391
10 4QIJ 1HA 2.69461
11 1VA6 P2S 3.207
12 1XDS SAM 3.207
13 1YB5 NAP 3.207
14 2Z8G GLC GLC BGC 3.207
15 5HW4 SAM 3.22581
16 3B1Q NOS 3.68098
17 5NNA BZM 3.78788
18 1KOR ARG 3.79009
19 1RY2 AMP 3.79009
20 3TTC ADP 3.80518
21 1N1G BCP 4.08163
22 2B5W NAP 4.37318
23 2J5B TYE 4.66472
24 2BJK NAD 4.66472
25 3FSY SCA 4.81928
26 2V3V MGD 4.95627
27 6GEW SAH 4.95627
28 6GEW SFG 4.95627
29 5N0O SAM 4.95627
30 2IV2 2MD 5.24781
31 3AXX CBI 5.53936
32 3QWI NAP 5.92593
33 4QDC ASD 6.41399
34 2B4Q NAP 7.24638
35 5W19 9TD 7.58017
36 4A0M NAD 9.62099
37 2NP9 YE1 9.62099
38 2QE0 NAP 13.7026
Pocket No.: 3; Query (leader) PDB : 4PTN; Ligand: GXV; Similar sites found with APoc: 5
This union binding pocket(no: 3) in the query (biounit: 4ptn.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 4DQ2 BTX 3.04878
2 3FP0 FP0 4.37318
3 3BBH SFG 5.53936
4 3DLG GWE 8.74636
5 3QV1 NAD 19.5122
Pocket No.: 4; Query (leader) PDB : 4PTN; Ligand: PYR; Similar sites found with APoc: 194
This union binding pocket(no: 4) in the query (biounit: 4ptn.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 3MJH GTP None
2 3BP1 GUN 1.37931
3 5AE9 OKO 1.45773
4 1JPA ANP 1.60256
5 4A4Z ANP 1.74927
6 3ZQ6 ADP ALF 1.85185
7 6EJI UD2 2.04082
8 1YQD NAP 2.04082
9 5W11 CTR 2.04082
10 5W5R PYR 2.04082
11 4LZJ 22H 2.31023
12 5F7R GLC GLC 2.33236
13 5KXQ GDP 2.33236
14 5KY4 GDP 2.33236
15 5LRT ADP 2.33236
16 4J75 TYM 2.33236
17 3TBK ANP 2.33236
18 5IBE 69M 2.33236
19 4E5N NAD 2.42424
20 5F1H 5U6 2.43902
21 1ZQ9 SAM 2.45614
22 1DL5 SAH 2.52366
23 1VQ2 DDN 2.59067
24 4ZS4 ATP 2.60586
25 3DZD ADP 2.62391
26 4LYA ATP 2.62391
27 3LDW ZOL 2.62391
28 3LDW IPE 2.62391
29 5LMC FMN 2.62391
30 5TT6 ATP 2.62391
31 6HOY TSN 2.64901
32 2J4K U5P 2.65487
33 154L NAG NAG NAG 2.7027
34 4CM9 YGL 2.77778
35 4CMI M4V 2.77778
36 3BMO AX4 2.77778
37 4CME NAP 2.77778
38 5TDF ADP 2.77778
39 5WRI A3P 2.8125
40 2EFX NFA 2.91545
41 1PFY MSP 2.91545
42 4NFE BEN 2.95359
43 5WRJ A3P 2.9703
44 2VZ0 D64 2.98507
45 2VZ0 NAP 2.98507
46 2GJN NIS 3.04878
47 5V49 MET 3.207
48 2ACV UDP 3.207
49 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 3.207
50 1YC5 NCA 3.25203
51 6EQS BV8 3.27273
52 1G63 FMN 3.31492
53 4XUB 43D 3.4188
54 5KBZ 3B2 3.49854
55 4WTV ATP 3.49854
56 6MVU K4V 3.49854
57 1MUU NAD 3.49854
58 1ICV FMN 3.49854
59 4HCX NDP 3.49854
60 4DVE BTN 3.53535
61 5VCV 1N1 3.53698
62 5O96 SAM 3.67347
63 3LU1 UD2 3.79009
64 5UN9 NHT 3.79009
65 1K7W AS1 3.79009
66 3B6Z CO7 3.79009
67 5Z21 NAI 3.79009
68 5JBE GLC GLC GLC GLC GLC 3.79009
69 5E4R NAP 3.79009
70 1KEV NDP 3.79009
71 5N5U AMP 3.82166
72 4NJH 2K8 3.91304
73 4NJH SAM 3.91304
74 2FSH ANP 4.08163
75 4IJP 1EH 4.08163
76 2QXL ATP 4.08163
77 6DF7 G9V 4.19162
78 4Y8D 49J 4.28571
79 1KQN NAD 4.30108
80 1S7G APR 4.34783
81 1Z45 UPG 4.37318
82 4CNG SAH 4.37318
83 5A89 ADP 4.48718
84 5A89 FMN 4.48718
85 4YSX FAD 4.60993
86 1OAA OAA 4.6332
87 1MWH GTG 4.66472
88 2WE0 UMP 4.66472
89 4UBT COA 4.66472
90 1EZ0 NAP 4.66472
91 4ZFL 4NK 4.70085
92 1I9G SAM 4.95627
93 4YNM SAM 4.95627
94 4YS0 ADP 4.95627
95 4XBA GMP 4.95627
96 4XBA 5GP 4.95627
97 5KY5 GDP 5
98 3HRD FAD 5.06757
99 3DCJ THH 5.11628
100 3EFS ATP 5.15021
101 2QRD ATP 5.15464
102 5JCA FAD 5.28169
103 1ZGD NAP 5.44872
104 6F7L FAD 5.53936
105 2H5Z CTO 5.7377
106 2XOC ADP 5.74713
107 3KO8 NAD 5.76923
108 6C90 ADP 5.76923
109 4C5N PXL 5.7971
110 4C5N ACP 5.7971
111 3HCN CHD 5.8309
112 3BK2 U5P 5.8309
113 5FI4 5XV 5.8309
114 4IGQ THR M3L GLN 5.8309
115 3ZIU LSS 5.8309
116 1ZB6 GST 5.86319
117 1ZB6 DIN 5.86319
118 4JEM C5P 5.88235
119 5M7S NHT 6.12245
120 4ZB6 GDS 6.27803
121 5L9O GOP 6.34328
122 5ML0 P2L 6.36364
123 2X7J TPP 6.41399
124 3BF1 PAU 6.4257
125 5IGL BMF 6.45161
126 3B7G ANP 6.52174
127 5FRD COA 6.53846
128 4J7U NAP 6.59722
129 4J7U YTZ 6.59722
130 2R3A SAM 6.66667
131 1PVN MZP 6.70554
132 4I54 1C1 6.70554
133 4HVA 4HV 6.79245
134 1P6O HPY 6.8323
135 4DO1 ANN 6.99708
136 6FFL GLC GLC GLC 7.28863
137 2P4Y C03 7.28863
138 1FNN ADP 7.28863
139 1HFE CYS 7.31707
140 1UHK CZN 7.32984
141 2X3F APC 7.36842
142 4L6C 0BT 7.42574
143 3GC8 B45 7.56757
144 6FW2 MTE 7.58017
145 3PNL ADP 7.58294
146 6FGL UO1 7.61905
147 1MID LAP 7.69231
148 5ABF XRJ 7.87172
149 1JG3 ADN 7.87172
150 1JG3 VAL TYR PRO IAS HIS ALA 7.87172
151 2BYC FMN 8.0292
152 4K6B GLU 8.07453
153 5EXT ADP 8.07692
154 1S8F GDP 8.16327
155 6FSG FMN 8.16327
156 1SQL GUN 8.21918
157 1BZY IMU 8.29493
158 4I4Z 2NE 8.36364
159 4GBM A3P 8.45481
160 5V22 SAH 8.45481
161 4XJC TTP 8.47458
162 3PP0 03Q 8.57988
163 5JLB SAH 8.60215
164 3TY5 ADP 8.74636
165 3VSV XYS 8.74636
166 2YK7 CSF 8.74636
167 3SXS PP2 8.95522
168 5BV3 M7G 9.0379
169 4B7H NDP 9.0379
170 4WOP CTP 9.33333
171 4A91 GLU 9.39597
172 2NP9 YE1 9.62099
173 4CS9 AMP 10.0529
174 2JFN GLU 10.1754
175 1DJN ADP 10.4956
176 4INI AMP 10.7692
177 6GR0 F8W 10.9195
178 5FDZ 5X0 10.9244
179 1ST0 GTG 11.276
180 5RHN 8BR 11.3043
181 4LX0 BEF GDP 11.3703
182 2YPO PHE 11.3703
183 5O1I 9GH 11.4155
184 1F9A ATP 11.9048
185 3BL7 DD1 12.6246
186 2FR6 CTN 13.0137
187 2Q7D ANP 13.1195
188 5AHM IMP 13.25
189 2W1A TSA 13.3333
190 2GK6 ADP 14.2857
191 4II2 ATP 14.4578
192 2RG0 CBI 14.8688
193 5NUL FMN 19.5652
194 4BMO FMN 22.6891
Pocket No.: 5; Query (leader) PDB : 4PTN; Ligand: GXV; Similar sites found with APoc: 22
This union binding pocket(no: 5) in the query (biounit: 4ptn.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 2WYV NAD 1.53257
2 4XAQ 40F 1.74927
3 1WP4 NDP 2.07612
4 4EUE NAI 2.62391
5 5GWT NAD 2.8777
6 1R6U TYM 3.207
7 5T2U NAP 3.22581
8 4JWF SAH 3.49854
9 3IAE D7K 3.79009
10 2Y5D NAP 3.79009
11 4ZUL UN1 4.08163
12 5FFF NAP 4.28016
13 9LDT NAD 4.51807
14 1YJQ NAP 5.28053
15 4Y1B NAP 5.53936
16 6F6E PLM 6.01266
17 2IXB NAD 6.12245
18 5XVH NAP 6.20915
19 5F7N NAG GAL FUC FUC A2G 7.28863
20 5XDR ADP 10.2041
21 1SJD NPG 10.4956
22 2FLI DX5 11.8182
Pocket No.: 6; Query (leader) PDB : 4PTN; Ligand: PYR; Similar sites found with APoc: 20
This union binding pocket(no: 6) in the query (biounit: 4ptn.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 1DY4 SNP 1.84332
2 5KY9 GDP 2.33236
3 3SLS 77D 2.96053
4 1CF2 NAP 2.96736
5 1QK3 5GP 3.00429
6 2ZKJ ADP 3.207
7 1CTU ZEB 3.40136
8 1XKV ATP 3.49854
9 1RP0 AHZ 3.52113
10 5Z99 SLB 3.79009
11 5XDT GDP 4.22078
12 2O07 SPD 4.66472
13 3TY3 GGG 5.8309
14 6FP4 FAD 6.41399
15 6G0X RAM GLC GLA NAG NDG NAG 6.41399
16 1IYK MIM 7.28863
17 4FMU 0UM 8.63309
18 2PID YSA 8.98876
19 6APV 3L4 9.72222
20 5XSS XYP 11.0759
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