Receptor
PDB id Resolution Class Description Source Keywords
2V9M 1.3 Å EC: 4.1.2.19 L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI ( MUTANT A87M-T109F-E192A) ESCHERICHIA COLI ENTROPY INDEX METAL-BINDING OLIGOMERIZATION ZINC LYASE ALDOLASE CLASS II CYTOPLASM CLEAVAGE OF L-RHAMNULOSE-1-PHOSPHATE TO DIHYDROXYACETONEPH BACTERIAL L-RHAMNOSE METABOLISM INTERFACE DESIGN SURFACE MUTATION 2-KETOSE DEGRADATION PROTEIN-PROTEIN INTERFACE RARE SUGAR AGGREGATION ZINC ENZYME FIBRILLATION RHAMNOSE METABOLISM PROTEIN ENGINEERING
Ref.: DESIGNED PROTEIN-PROTEIN ASSOCIATION. SCIENCE V. 319 206 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1276;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
CIT A:1278;
Valid;
none;
submit data
192.124 C6 H8 O7 C(C(=...
EDO A:1279;
A:1280;
A:1281;
A:1282;
B:1277;
B:1278;
B:1279;
B:1280;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
ZN A:1275;
A:1277;
B:1275;
B:1276;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2V9M 1.3 Å EC: 4.1.2.19 L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI ( MUTANT A87M-T109F-E192A) ESCHERICHIA COLI ENTROPY INDEX METAL-BINDING OLIGOMERIZATION ZINC LYASE ALDOLASE CLASS II CYTOPLASM CLEAVAGE OF L-RHAMNULOSE-1-PHOSPHATE TO DIHYDROXYACETONEPH BACTERIAL L-RHAMNOSE METABOLISM INTERFACE DESIGN SURFACE MUTATION 2-KETOSE DEGRADATION PROTEIN-PROTEIN INTERFACE RARE SUGAR AGGREGATION ZINC ENZYME FIBRILLATION RHAMNOSE METABOLISM PROTEIN ENGINEERING
Ref.: DESIGNED PROTEIN-PROTEIN ASSOCIATION. SCIENCE V. 319 206 2008
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2V2A - 13P C3 H7 O6 P C(C(=O)COP....
2 2V9N - CIT C6 H8 O7 C(C(=O)O)C....
3 1OJR - 2HA C3 H6 O3 C(C(=O)CO)....
4 2V9M - CIT C6 H8 O7 C(C(=O)O)C....
5 2UYV - TLA C4 H6 O6 [C@@H]([C@....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2V2A - 13P C3 H7 O6 P C(C(=O)COP....
2 2V9N - CIT C6 H8 O7 C(C(=O)O)C....
3 1OJR - 2HA C3 H6 O3 C(C(=O)CO)....
4 2V9M - CIT C6 H8 O7 C(C(=O)O)C....
5 2UYV - TLA C4 H6 O6 [C@@H]([C@....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2V2A - 13P C3 H7 O6 P C(C(=O)COP....
2 2V9N - CIT C6 H8 O7 C(C(=O)O)C....
3 1OJR - 2HA C3 H6 O3 C(C(=O)CO)....
4 2V9M - CIT C6 H8 O7 C(C(=O)O)C....
5 2UYV - TLA C4 H6 O6 [C@@H]([C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CIT; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 CIT 1 1
2 HCA 0.576923 0.884615
3 MAH 0.44 0.807692
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2V9M; Ligand: CIT; Similar sites found: 187
This union binding pocket(no: 1) in the query (biounit: 2v9m.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.007049 0.44553 None
2 1UO4 PIH 0.009371 0.42982 None
3 1C1L GAL BGC 0.003708 0.42605 None
4 1PTR PRB 0.009192 0.40847 None
5 3QDV A2G 0.01938 0.40643 None
6 2YVF FAD 0.04703 0.40223 1.09489
7 2B7N NTM 0.00619 0.40416 1.0989
8 3CXO 1N5 0.000006305 0.54055 1.45985
9 1JA9 NDP 0.00009912 0.52802 1.45985
10 1JA9 PYQ 0.0000716 0.49377 1.45985
11 3CXO 3LR 0.000229 0.47316 1.45985
12 4AP9 1PS 0.000003674 0.44324 1.49254
13 5A2J ALA PRO ASP THR ARG PRO 0.01896 0.40353 1.63934
14 3NOJ PYR 0.001514 0.42625 1.68067
15 1W55 C 0.00006108 0.52101 1.82482
16 1MG1 MAL 0.004475 0.41124 1.82482
17 1FX8 BOG 0.0001924 0.4088 1.82482
18 4R33 SAH 0.01399 0.40496 1.82482
19 4R33 TRP 0.01399 0.40496 1.82482
20 2Q1A 2KT 0.00006445 0.40083 1.82482
21 4B16 NAG 0.005067 0.44338 1.8797
22 1JLV GSH 0.02013 0.41011 1.91388
23 4F8L GAL 0.01136 0.43445 2.06897
24 1R0X ATP 0.0001686 0.48477 2.18978
25 2IMP LAC 0.000001756 0.45847 2.18978
26 3UDG TMP 0.003712 0.44128 2.18978
27 4OYA 1VE 0.01688 0.43841 2.18978
28 1KC7 PPR 0.004702 0.42146 2.18978
29 3QV9 QV7 0.002893 0.4178 2.18978
30 1B9I PXG 0.0038 0.41575 2.18978
31 1X54 4AD 0.005686 0.41037 2.18978
32 3O03 GCO 0.01674 0.40954 2.18978
33 4USQ FAD 0.01343 0.4068 2.18978
34 1Y7P RIP 0.001519 0.45125 2.24215
35 3VKX T3 0.0001981 0.46163 2.29885
36 3KJI ADP 0.004591 0.40119 2.3622
37 1SBZ FMN 0.00004437 0.50728 2.53807
38 4N02 FNR 0.00008471 0.51892 2.55474
39 4HZX G39 0.0001089 0.50086 2.55474
40 2BO4 FLC 0.00661 0.41487 2.55474
41 1NML CIT 0.002741 0.41295 2.55474
42 4M7F BM3 0.00008769 0.47243 2.65487
43 2QIA U20 0.03085 0.40633 2.67176
44 2FWP ICR 0.000004317 0.55423 2.73224
45 2FWP CIT 0.00006899 0.49776 2.73224
46 4COQ SAN 0.008521 0.40394 2.83401
47 2FMD MAN MAN 0.00007192 0.4777 2.91667
48 2NLI LAC 0.00001604 0.54853 2.91971
49 2NLI FMN 0.00001604 0.54853 2.91971
50 2GN2 C5P 0.000003095 0.46616 2.91971
51 3VOZ 04A 0.00009711 0.41737 2.91971
52 2Q8H TF4 0.01555 0.4111 2.91971
53 2XRH NIO 0.01178 0.40367 3
54 3H86 AP5 0.004785 0.43724 3.125
55 1SS4 CIT 0.02541 0.44673 3.26797
56 4TSK NDP 0.0002078 0.50541 3.28467
57 1HFA PIO 0.02199 0.444 3.28467
58 4TSK TLA 0.001088 0.43166 3.28467
59 2EB5 OXL 0.005129 0.4134 3.37079
60 1OMZ UD2 0.00004523 0.5221 3.64964
61 1A5Z OXM 0.0001542 0.49725 3.64964
62 1Z6K OAA 0.0001681 0.44295 3.64964
63 3IHB TRS 0.03034 0.42846 3.64964
64 3U1T MLI 0.003743 0.42587 3.64964
65 1A5Z FBP 0.00004225 0.41683 3.64964
66 1XHL NDP 0.01232 0.40611 3.64964
67 4ODV GP1 Z9M 0.001341 0.48392 3.72093
68 1JOT GAL A2G 0.002345 0.40498 3.7594
69 1Y1A GSH 0.03449 0.40282 3.82514
70 1O68 KIV 0.001163 0.42777 4
71 1Z42 HBA 0.004379 0.46239 4.0146
72 1LTH OXM 0.00007481 0.46065 4.0146
73 1LTH FBP 0.0004761 0.45758 4.0146
74 1VBH PEP 0.002461 0.4207 4.0146
75 1I0Z OXM 0.01859 0.40731 4.0146
76 3SCH TB6 0.004443 0.41607 4.0404
77 2ALG DAO 0.003575 0.41401 4.34783
78 3EYK EYK 0.0006955 0.45054 4.37956
79 1GPJ CIT 0.003248 0.4219 4.37956
80 2PAR TMP 0.002309 0.44812 4.47761
81 1P9P SAH 0.00687 0.40386 4.5977
82 4AF5 CIT 0.004233 0.41697 4.73684
83 1OFH ADP 0.002336 0.42747 4.74453
84 1PEA ACM 0.006138 0.42314 4.74453
85 3L24 GOA 0.01268 0.41541 4.74453
86 2AEB ABH 0.007089 0.40804 4.74453
87 1UFY MLI 0.001665 0.43432 4.91803
88 2OFD NGA 0.001193 0.44052 4.92958
89 2OFE NAG 0.001949 0.43139 4.92958
90 1H9G COA MYR 0.0005557 0.45424 4.93827
91 2VQ5 LDP 0.004374 0.43783 4.97512
92 4U36 TNR 0.0000002054 0.44731 5
93 3R51 MMA 0.01427 0.41291 5
94 2P1M IHP 0.01039 0.40134 5
95 1AX2 NDG GAL 0.005047 0.40238 5.02092
96 2VMD MBG 0.0002862 0.4951 5.05837
97 1Q3Q ANP 0.00009054 0.52142 5.10949
98 3K3G MMU 0.0003205 0.45355 5.10949
99 3VCA PRO 0.002247 0.4193 5.10949
100 2FGQ MLT 0.005194 0.41317 5.10949
101 2D37 FMN 0.006862 0.41007 5.11364
102 2D37 NAD 0.00743 0.41007 5.11364
103 1C3M MAN MAN 0.0008751 0.40201 5.44218
104 2YD6 FLC 0.0025 0.46884 5.47445
105 3CL7 HYN 0.0005805 0.45004 5.47445
106 4MOB ADP 0.00004095 0.43964 5.47445
107 1JN2 SFP 0.0007927 0.40418 5.48523
108 4DN8 BMA 0.005679 0.4115 5.76923
109 1SAZ ACP 0.0004948 0.50041 5.83942
110 3L6R MLI 0.006442 0.41536 5.83942
111 3KPE TM3 0.008117 0.40485 5.88235
112 1FNZ A2G 0.000005754 0.42722 5.90717
113 1DUC DUD 0.00004989 0.40835 5.97015
114 2H6B 3C4 0.001244 0.46926 6
115 3PAK MAN 0.000371 0.44417 6.08108
116 3E81 SLB 0.006252 0.40398 6.09756
117 4TMK T5A 0.0006051 0.51113 6.10329
118 1UQX MMA 0.0001296 0.47608 6.19469
119 4G1V FAD 0.00004424 0.55848 6.20438
120 3FPZ AHZ 0.00004283 0.55059 6.20438
121 2BGM NAJ 0.00004279 0.53588 6.20438
122 2BGM MAX 0.0006267 0.44871 6.20438
123 1RRC ADP 0.001277 0.4328 6.20438
124 3K87 FAD 0.02374 0.42579 6.48649
125 3ZPG 5GP 0.01876 0.40712 6.5445
126 2VJJ RAM GLC GAL NAG NAG GLC 0.00971 0.42633 6.56934
127 2IZ1 ATR 0.008546 0.40389 6.56934
128 2DWU DGL 0.003799 0.40207 6.56934
129 4IS0 1R4 0.01353 0.40968 6.639
130 1QB7 ADE 0.00294 0.40133 6.77966
131 2BLE 5GP 0.00000355 0.58596 6.93431
132 3SJ0 DXC 0.01129 0.40448 7.04225
133 3V0W PA1 GLC GLC GLC GM0 GLA GM0 GMH KDO KDO 0.002658 0.46267 7.07547
134 2NZ2 ASP 0.00005769 0.47967 7.29927
135 1ZFJ IMP 0.007293 0.45479 7.29927
136 1ULE GLA GAL NAG 0.009727 0.40147 7.33333
137 1NPL MAN 0.008301 0.4006 7.33945
138 1Y0L HAN 0.02565 0.40751 7.52212
139 2XI7 XI7 0.02594 0.41521 7.6087
140 2DUA OXL 0.000007823 0.5153 7.66423
141 4AF0 MOA 0.00001096 0.40466 7.66423
142 4Q3F TLA 0.002258 0.42866 7.69231
143 5DUB GLY 5GG GLY ALA 0.01651 0.4064 7.94393
144 5DTF 5CT 0.01723 0.40551 7.94393
145 1V5F FAD 0.002253 0.49355 8.0292
146 1V5F TPP 0.002253 0.49355 8.0292
147 3LTW HLZ 0.00496 0.41402 8.0292
148 4GYW UDP 0.01041 0.41031 8.0292
149 3F81 STT 0.01914 0.40015 8.19672
150 1TV5 N8E 0.00003089 0.42682 8.39416
151 1A8S PPI 0.0001405 0.44491 8.42491
152 3S9K CIT 0.02191 0.41664 8.47458
153 1A59 CIT 0.01108 0.40485 8.75912
154 3CBG FER 0.002603 0.44874 9.05172
155 3CBG 4FE 0.01289 0.42277 9.05172
156 3A8U PLP 0.00002528 0.50447 9.1314
157 1NME 159 0.00005745 0.47105 9.78261
158 1F1V DHY 0.001819 0.41438 9.85401
159 3ZGE ASP 0.01051 0.41228 9.85401
160 3GD8 BOG 0.000006564 0.5607 9.86547
161 1NZY BCA 0.00608 0.41362 10.0372
162 4K7O EKZ 0.01414 0.40011 10.119
163 3MAG 3MA 0.02634 0.40692 10.219
164 1NXJ GLV 0.001577 0.41677 10.3825
165 1NXJ TLA 0.0004756 0.40146 10.3825
166 2PWY SAH 0.007968 0.40293 10.4651
167 4CIB 7UZ 0.005827 0.40525 11.6788
168 1XX4 BAM 0.0008814 0.43577 11.8774
169 3RF4 FUN 0.004762 0.40339 12.069
170 3SUC ATP 0.000009709 0.54402 12.4088
171 2BZ1 TAU 0.01001 0.4374 12.7551
172 1H8P PC 0.003557 0.44218 12.844
173 1P72 THM 0.004821 0.40318 13.1387
174 4LO6 SIA GAL 0.003644 0.42993 13.1579
175 3I8T LBT 0.00001709 0.50068 14.0244
176 1NU4 MLA 0.001177 0.42166 14.433
177 1Y2W NAG 0.00121 0.44026 14.7887
178 2ZWS PLM 0.002892 0.46615 14.9635
179 1HQL GLA MBG 0.01422 0.40001 15.1751
180 1BTN I3P 0.000195 0.53257 16.9811
181 2XDQ MGX 0.01794 0.40807 17.1533
182 2HVK TBA 0.00007886 0.49097 18.3962
183 1FWE HAE 0.0002447 0.44789 21
184 2P4T NAP 0.00001491 0.52516 24.1935
185 1H16 DTL 0.02505 0.40098 25.1825
186 1JGS SAL 0.03233 0.41005 32.6087
187 4HGP KDO 0.005292 0.4249 33.8889
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