Receptor
PDB id Resolution Class Description Source Keywords
3Q9N 2 Å NON-ENZYME: BINDING IN SILICO AND IN VITRO CO-EVOLUTION OF A HIGH AFFINITY COMPL PROTEIN-PROTEIN INTERFACE ESCHERICHIA COLI STRUCTURAL GENOMICS ISRAEL STRUCTURAL PROTEOMICS CENTER ISBINDING DESIGNED ANKYRIN REPEAT PROTEIN BINDING DE NOVO P
Ref.: A DE NOVO PROTEIN BINDING PAIR BY COMPUTATIONAL DES DIRECTED EVOLUTION. MOL.CELL V. 42 250 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CMS A:1071;
Invalid;
none;
submit data
132.118 C4 H8 N2 O3 CN(CC...
COA A:1072;
B:1072;
Valid;
Valid;
none;
none;
Kd = 130 nM
767.534 C21 H36 N7 O16 P3 S CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3Q9N 2 Å NON-ENZYME: BINDING IN SILICO AND IN VITRO CO-EVOLUTION OF A HIGH AFFINITY COMPL PROTEIN-PROTEIN INTERFACE ESCHERICHIA COLI STRUCTURAL GENOMICS ISRAEL STRUCTURAL PROTEOMICS CENTER ISBINDING DESIGNED ANKYRIN REPEAT PROTEIN BINDING DE NOVO P
Ref.: A DE NOVO PROTEIN BINDING PAIR BY COMPUTATIONAL DES DIRECTED EVOLUTION. MOL.CELL V. 42 250 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 473 families.
1 3Q9N Kd = 130 nM COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
2 3Q9U Kd = 130 nM COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 355 families.
1 3Q9N Kd = 130 nM COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
2 3Q9U Kd = 130 nM COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 3Q9N Kd = 130 nM COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
2 3Q9U Kd = 130 nM COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: COA; Similar ligands found: 197
No: Ligand ECFP6 Tc MDL keys Tc
1 COA 1 1
2 0T1 0.894737 0.976744
3 DCA 0.893805 0.954023
4 COS 0.887931 0.977012
5 ETB 0.877193 0.920455
6 CAO 0.871795 0.965909
7 AMX 0.871795 0.988235
8 30N 0.871795 0.913979
9 CMX 0.864407 0.976744
10 SCO 0.864407 0.976744
11 FAM 0.857143 0.954545
12 ACO 0.857143 0.965909
13 FCX 0.857143 0.94382
14 HAX 0.85 0.954545
15 3KK 0.842975 0.977012
16 FYN 0.842975 1
17 CA6 0.836066 0.885417
18 SOP 0.836066 0.977012
19 MCD 0.836066 0.954545
20 COK 0.836066 0.977012
21 OXK 0.836066 0.977012
22 NMX 0.829268 0.903226
23 CO6 0.829268 0.977012
24 CMC 0.829268 0.977012
25 1VU 0.829268 0.965909
26 CAJ 0.822581 0.954545
27 SCD 0.822581 0.976744
28 2MC 0.822581 0.934066
29 2CP 0.81746 0.965909
30 BCO 0.816 0.977012
31 3HC 0.816 0.988372
32 1HE 0.816 0.955056
33 MLC 0.816 0.977012
34 A1S 0.816 0.977012
35 IVC 0.816 0.988372
36 COD 0.810345 0.988235
37 CAA 0.809524 0.988372
38 COO 0.809524 0.977012
39 MCA 0.809524 0.965909
40 YE1 0.809524 0.965517
41 SCA 0.80315 0.977012
42 MC4 0.80315 0.923913
43 IRC 0.796875 0.988372
44 3CP 0.796875 0.977012
45 CA8 0.796875 0.885417
46 BYC 0.796875 0.977012
47 COW 0.796875 0.965909
48 2KQ 0.796875 0.955056
49 COF 0.796875 0.955056
50 HGG 0.796875 0.977012
51 1GZ 0.796875 0.965909
52 4CA 0.790698 0.965909
53 FAQ 0.790698 0.977012
54 BCA 0.790698 0.965909
55 GRA 0.784615 0.977012
56 HXC 0.784615 0.955056
57 1CV 0.781955 0.977012
58 TGC 0.778626 0.965909
59 1CZ 0.772727 0.965909
60 CO8 0.772727 0.955056
61 S0N 0.772727 0.954545
62 2NE 0.772727 0.955056
63 CIC 0.772727 0.977012
64 0FQ 0.766917 0.977012
65 ST9 0.766917 0.955056
66 4CO 0.766917 0.965909
67 UCC 0.766917 0.955056
68 MFK 0.766917 0.955056
69 DCC 0.766917 0.955056
70 MYA 0.766917 0.955056
71 5F9 0.766917 0.955056
72 01A 0.761194 0.934066
73 0ET 0.761194 0.955056
74 CS8 0.755556 0.944444
75 WCA 0.755556 0.955056
76 4KX 0.75 0.944444
77 UOQ 0.75 0.955056
78 NHW 0.75 0.955056
79 HDC 0.75 0.955056
80 NHM 0.75 0.955056
81 HFQ 0.744526 0.955056
82 MRS 0.744526 0.955056
83 MRR 0.744526 0.955056
84 DAK 0.73913 0.944444
85 YNC 0.73913 0.965909
86 8Z2 0.733813 0.944444
87 NHQ 0.723404 0.988372
88 1HA 0.713287 0.955056
89 01K 0.708333 0.977012
90 COT 0.703448 0.977012
91 CCQ 0.695652 0.934066
92 CA3 0.693878 0.977012
93 CA5 0.671053 0.934066
94 UCA 0.666667 0.955056
95 93P 0.666667 0.965909
96 CO7 0.664234 0.977012
97 93M 0.64557 0.965909
98 OXT 0.634146 0.913979
99 5TW 0.607143 0.913979
100 4BN 0.607143 0.913979
101 PAP 0.603604 0.811765
102 JBT 0.598837 0.894737
103 BSJ 0.592814 0.944444
104 HMG 0.581081 0.943182
105 COA MYR 0.573333 0.922222
106 PLM COA 0.573333 0.922222
107 COA PLM 0.573333 0.922222
108 A3P 0.54955 0.8
109 PPS 0.547009 0.752688
110 0WD 0.521739 0.788889
111 RFC 0.490683 0.955056
112 SFC 0.490683 0.955056
113 191 0.490196 0.865979
114 3AM 0.482143 0.788235
115 PTJ 0.48062 0.872093
116 ACE SER ASP ALY THR NH2 COA 0.478261 0.932584
117 4PS 0.477477 0.682353
118 A22 0.468254 0.813953
119 A2D 0.465517 0.802326
120 PUA 0.462585 0.820225
121 PAJ 0.460938 0.883721
122 AGS 0.459016 0.806818
123 SAP 0.459016 0.806818
124 ATR 0.459016 0.8
125 3OD 0.458015 0.825581
126 ADP 0.453782 0.823529
127 A2R 0.448819 0.813953
128 BA3 0.445378 0.802326
129 NA7 0.442748 0.858824
130 OAD 0.442748 0.825581
131 ATP 0.442623 0.823529
132 AP5 0.441667 0.802326
133 B4P 0.441667 0.802326
134 APR 0.439024 0.802326
135 5FA 0.439024 0.823529
136 2A5 0.439024 0.847059
137 AQP 0.439024 0.823529
138 AR6 0.439024 0.802326
139 AN2 0.438017 0.813953
140 48N 0.435714 0.808989
141 M33 0.434426 0.813953
142 SRP 0.429688 0.837209
143 ANP 0.428571 0.804598
144 ADQ 0.427481 0.804598
145 YLB 0.426573 0.908046
146 YLP 0.425532 0.886364
147 5AL 0.425197 0.813953
148 7D3 0.425 0.793103
149 AD9 0.424 0.804598
150 APU 0.423611 0.786517
151 7D4 0.422764 0.793103
152 CA0 0.422764 0.804598
153 25L 0.422222 0.813953
154 ATF 0.421875 0.795455
155 NJP 0.421769 0.806818
156 A2P 0.421488 0.788235
157 A A A 0.421053 0.813953
158 8QN 0.419847 0.813953
159 PNS 0.419643 0.682353
160 ACP 0.419355 0.825581
161 NDP 0.417808 0.788889
162 ACQ 0.417323 0.825581
163 A1R 0.416667 0.882353
164 ATP A A A 0.416058 0.770115
165 A 0.415254 0.8
166 AMP 0.415254 0.8
167 FYA 0.414815 0.813953
168 1ZZ 0.414815 0.842697
169 TXA 0.414815 0.816092
170 NB8 0.414815 0.808989
171 AHX 0.413534 0.829545
172 DLL 0.413534 0.793103
173 00A 0.413534 0.758242
174 PAX 0.412903 0.793478
175 OMR 0.409722 0.853933
176 25A 0.409091 0.802326
177 OOB 0.409091 0.793103
178 NPW 0.408163 0.822222
179 WAQ 0.407407 0.860465
180 A A 0.407407 0.781609
181 TAT 0.40625 0.816092
182 4AD 0.406015 0.827586
183 AMO 0.406015 0.837209
184 YAP 0.405797 0.806818
185 FA5 0.405797 0.816092
186 TXP 0.405405 0.829545
187 ABM 0.404959 0.781609
188 PRX 0.404762 0.825581
189 ME8 0.404412 0.842697
190 BIS 0.404412 0.818182
191 AFH 0.404255 0.78022
192 J7V 0.403846 0.778947
193 NAI 0.402778 0.777778
194 ODP 0.402685 0.78022
195 ADX 0.4 0.752688
196 SRA 0.4 0.784091
197 AU1 0.4 0.804598
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3Q9N; Ligand: COA; Similar sites found: 104
This union binding pocket(no: 1) in the query (biounit: 3q9n.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2FKA BEF 0.01026 0.44029 2.32558
2 2VT3 ATP 0.0004015 0.48709 2.83688
3 4G9N NGA 0.02337 0.40806 2.83688
4 1JT2 FER 0.01816 0.41635 3.5461
5 4K7O EKZ 0.006528 0.43828 3.57143
6 2IZ1 ATR 0.006669 0.44152 4.25532
7 2Q0L NAP 0.006374 0.42066 4.25532
8 2WPF WPF 0.01992 0.41601 4.25532
9 2WPF FAD 0.02368 0.41255 4.25532
10 3LRE ADP 0.03689 0.40565 4.25532
11 1LSS NAD 0.01019 0.40125 4.28571
12 4KOA NDP 0.008275 0.41181 4.43038
13 1BW9 NAD 0.004182 0.41167 4.43038
14 2AF6 BRU 0.006506 0.44509 4.96454
15 3H8V ATP 0.003043 0.42785 4.96454
16 2AG8 NAP 0.002616 0.4236 5.06329
17 3HVJ 705 0.002417 0.42248 5.06329
18 1U6R IOM 0.02711 0.40907 5.06329
19 5N53 8NB 0.0009302 0.49063 5.67376
20 1KYQ NAD 0.001041 0.45286 5.67376
21 4RDH AMP 0.001889 0.44527 5.67376
22 4D79 ATP 0.002232 0.43386 5.67376
23 4RDI ATP 0.00334 0.42605 5.67376
24 4K28 NAD 0.001451 0.42111 5.67376
25 2HJR APR 0.006074 0.40192 5.67376
26 3WLE NAD 0.0002266 0.40579 5.6962
27 1A5Z NAD 0.006645 0.40321 5.6962
28 3EGI ADP 0.03913 0.40079 5.6962
29 4URG C2E 0.04311 0.40042 5.6962
30 1LTH NAD 0.001507 0.42362 6.32911
31 1EBF NAD 0.002228 0.40296 6.32911
32 5E5U MLI 0.001643 0.46323 6.38298
33 3ITJ CIT 0.01136 0.4282 6.38298
34 4RL4 PPV 0.01564 0.41257 6.38298
35 1I9G SAM 0.005544 0.40961 6.38298
36 1X14 NAD 0.01221 0.40409 6.38298
37 2IMG MLT 0.04149 0.40056 6.38298
38 2O4C NAD 0.00555 0.40074 6.57895
39 5KVA SAM 0.001635 0.42882 6.96203
40 1KC7 PPR 0.03932 0.40569 6.96203
41 4W6Z 8ID 0.006781 0.4031 6.96203
42 5BW4 SAM 0.01371 0.40177 6.96203
43 5OFW 9TW 0.002727 0.46212 7.0922
44 5KVS NAP 0.0008998 0.43268 7.0922
45 3DXY SAM 0.007462 0.42526 7.0922
46 3CBG SAH 0.00839 0.41154 7.0922
47 3SQP FAD 0.02188 0.43104 7.80142
48 3B1F NAD 0.00317 0.41673 7.80142
49 1O0S NAI 0.0038 0.41033 7.80142
50 4YMH SAH 0.006298 0.40723 7.80142
51 1J5P NAD 0.002791 0.40288 7.80142
52 4II2 ATP 0.006089 0.40786 8.22785
53 2NU8 COA 0.000843 0.42727 8.51064
54 3OJO NAD 0.003081 0.41409 8.51064
55 2G5C NAD 0.002745 0.40303 8.86076
56 1H2B NAJ 0.0006735 0.40213 8.86076
57 1X87 NAD 0.002033 0.42154 9.21986
58 3CIF G3H 0.002616 0.41877 9.21986
59 3CIF NAD 0.001912 0.41638 9.21986
60 2YX1 SFG 0.0179 0.40307 9.21986
61 1VJT NAD 0.009654 0.40228 9.21986
62 1I36 NAP 0.006352 0.40111 9.21986
63 3OBT SLB 0.03571 0.40287 9.49367
64 3ICS ADP 0.00335 0.44223 10.1266
65 3ICT ADP 0.005955 0.43004 10.1266
66 1LDN NAD 0.002575 0.41403 10.6383
67 1ZH8 NAP 0.002013 0.41403 10.6383
68 2PV7 NAD 0.001507 0.41257 10.6383
69 3OA2 NAD 0.0005749 0.42381 10.7595
70 1OBB NAD 0.001683 0.42168 10.7595
71 5DYO FLU 0.03586 0.40636 10.7595
72 1MV8 NAD 0.003535 0.40297 10.7595
73 2CDU ADP 0.003582 0.42841 11.3924
74 3V1Y NAD 0.001636 0.41603 11.3924
75 3H9E NAD 0.001843 0.41401 11.3924
76 5AYV NAP 0.003184 0.4135 11.3924
77 5N2I NAP 0.00779 0.40326 11.3924
78 3NJ4 NAD 0.02001 0.42261 12.0253
79 2F1K NAP 0.002458 0.40913 12.0253
80 3G89 SAM 0.02006 0.4007 12.0567
81 2NXE SAM 0.0005927 0.45954 12.766
82 1V59 NAD 0.003813 0.43949 12.766
83 3EGV SAH 0.00257 0.43498 12.766
84 1D1T NAD 0.001177 0.40694 12.766
85 4CIB 7UZ 0.01801 0.42155 13.2911
86 1ZQ9 SAM 0.003534 0.42495 14.1844
87 1UP7 NAD 0.002773 0.40994 14.1844
88 3WV8 ATP 0.005429 0.41324 15.6028
89 1WDK NAD 0.00217 0.42036 15.8228
90 1OMO NAD 0.004702 0.40361 15.8228
91 2VYN NAD 0.002274 0.40099 16.3121
92 5CAE COA 0.0008305 0.43409 16.4557
93 1Y8Q ATP 0.005417 0.40111 17.7305
94 3WCS MAN NAG GAL 0.01653 0.41219 19.1489
95 3WCS MAN NAG 0.02503 0.41112 19.1489
96 2HK9 ATR 0.01868 0.40953 21.9858
97 1P77 ATR 0.03592 0.40278 21.9858
98 1DSS NAD 0.00223 0.4137 23.4043
99 1JH7 UVC 0.035 0.40652 24.6835
100 3W9F I3P 0.005775 0.43289 25.9494
101 3F81 STT 0.03134 0.4062 25.9494
102 5JE8 NAD 0.00102 0.4272 28.3688
103 4XZ3 COA 0.000002437 0.5419 34.0426
104 4XYM COA 0.00004356 0.4081 34.7518
Pocket No.: 2; Query (leader) PDB : 3Q9N; Ligand: COA; Similar sites found: 23
This union binding pocket(no: 2) in the query (biounit: 3q9n.bio2) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3I9U DTU 0.03409 0.40414 3.16456
2 5E9W SAH 0.01988 0.40013 4.25532
3 1LJ8 NAD 0.009171 0.40003 4.96454
4 3B50 SLB 0.02296 0.40391 5.06329
5 3X0D SAH 0.009653 0.40499 5.67376
6 1BZL FAD 0.01553 0.41701 5.6962
7 1JG3 ADN 0.007681 0.41263 5.6962
8 3FUU ADN 0.008839 0.40669 5.6962
9 4AZW SAM 0.01006 0.40419 6.32911
10 1GR0 NAD 0.0007943 0.40448 7.59494
11 1LVL NAD 0.008386 0.40462 10.1266
12 1MUU NAD 0.004495 0.40173 10.1266
13 2QL9 CIT 0.04376 0.40166 11.3475
14 2DFV NAD 0.003823 0.40451 13.4752
15 1WP4 NDP 0.003412 0.40377 13.4752
16 2CVZ NDP 0.004547 0.40153 13.4752
17 4AZT SAM 0.01415 0.40064 13.4752
18 2VVG ADP 0.03806 0.40769 14.1844
19 4YCA NDP 0.004689 0.401 14.1844
20 3K4Z CBI 0.0283 0.412 15.8228
21 3SSO SAH 0.009027 0.40323 16.3121
22 2PWY SAH 0.003928 0.4126 19.8582
23 4C4A SAH 0.008983 0.40637 20.2532
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