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Receptor
PDB id Resolution Class Description Source Keywords
4XTX 2.3 Å EC: 6.3.4.15 MYCOBACTERIUM TUBERCULOSIS BIOTIN LIGASE COMPLEXED WITH BISU INHIBITOR 57 WITH AZIDE IN PLACE OF RIBOSE 2'OH MYCOBACTERIUM TUBERCULOSIS BIOTIN-PROTEIN LIGASE BISUBSTRATE INHIBITOR LIGASE-LIGASE COMPLEX
Ref.: TARGETING MYCOBACTERIUM TUBERCULOSIS BIOTIN PROTEIN (MTBPL) WITH NUCLEOSIDE-BASED BISUBSTRATE ADENYLATI INHIBITORS. J.MED.CHEM. V. 58 7349 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
590 B:300;
A:301;
Valid;
Valid;
none;
none;
Kd = 0.027 nM
597.628 C20 H27 N11 O7 S2 c1nc(...
EDO A:302;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4XTX 2.3 Å EC: 6.3.4.15 MYCOBACTERIUM TUBERCULOSIS BIOTIN LIGASE COMPLEXED WITH BISU INHIBITOR 57 WITH AZIDE IN PLACE OF RIBOSE 2'OH MYCOBACTERIUM TUBERCULOSIS BIOTIN-PROTEIN LIGASE BISUBSTRATE INHIBITOR LIGASE-LIGASE COMPLEX
Ref.: TARGETING MYCOBACTERIUM TUBERCULOSIS BIOTIN PROTEIN (MTBPL) WITH NUCLEOSIDE-BASED BISUBSTRATE ADENYLATI INHIBITORS. J.MED.CHEM. V. 58 7349 2015
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4XU1 Kd = 0.324 nM 44O C20 H29 N9 O6 S2 c1nc(c2c(n....
2 4XTW Kd = 0.933 nM 44M C20 H28 N12 O6 S2 c1nc(c2c(n....
3 4XTX Kd = 0.027 nM 590 C20 H27 N11 O7 S2 c1nc(c2c(n....
4 3RUX Kd = 0.53 nM BS5 C20 H29 N9 O7 S2 c1nc(c2c(n....
5 4XTZ Kd = 0.153 nM 594 C20 H27 F N8 O7 S2 c1nc(c2c(n....
6 4XTV Kd = 0.54 nM 44K C21 H31 N9 O4 S2 c1nc(c2c(n....
7 4OP0 - BT5 C20 H28 N7 O9 P S c1nc(c2c(n....
8 4XU2 Kd = 0.592 nM 44Q C20 H29 N9 O6 S2 c1nc(c2c(n....
9 4XU3 Kd = 0.315 nM 44R C18 H27 N9 O5 S2 c1nc(c2c(n....
10 4XTY Kd = 0.614 nM 44L C20 H28 F N9 O6 S2 c1nc(c2c(n....
11 4XU0 Kd = 0.769 nM 44N C21 H30 N8 O8 S2 C[C@]1([C@....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4XU1 Kd = 0.324 nM 44O C20 H29 N9 O6 S2 c1nc(c2c(n....
2 4XTW Kd = 0.933 nM 44M C20 H28 N12 O6 S2 c1nc(c2c(n....
3 4XTX Kd = 0.027 nM 590 C20 H27 N11 O7 S2 c1nc(c2c(n....
4 3RUX Kd = 0.53 nM BS5 C20 H29 N9 O7 S2 c1nc(c2c(n....
5 4XTZ Kd = 0.153 nM 594 C20 H27 F N8 O7 S2 c1nc(c2c(n....
6 4XTV Kd = 0.54 nM 44K C21 H31 N9 O4 S2 c1nc(c2c(n....
7 4OP0 - BT5 C20 H28 N7 O9 P S c1nc(c2c(n....
8 4XU2 Kd = 0.592 nM 44Q C20 H29 N9 O6 S2 c1nc(c2c(n....
9 4XU3 Kd = 0.315 nM 44R C18 H27 N9 O5 S2 c1nc(c2c(n....
10 4XTY Kd = 0.614 nM 44L C20 H28 F N9 O6 S2 c1nc(c2c(n....
11 4XU0 Kd = 0.769 nM 44N C21 H30 N8 O8 S2 C[C@]1([C@....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4XU1 Kd = 0.324 nM 44O C20 H29 N9 O6 S2 c1nc(c2c(n....
2 4XTW Kd = 0.933 nM 44M C20 H28 N12 O6 S2 c1nc(c2c(n....
3 4XTX Kd = 0.027 nM 590 C20 H27 N11 O7 S2 c1nc(c2c(n....
4 3RUX Kd = 0.53 nM BS5 C20 H29 N9 O7 S2 c1nc(c2c(n....
5 4XTZ Kd = 0.153 nM 594 C20 H27 F N8 O7 S2 c1nc(c2c(n....
6 4XTV Kd = 0.54 nM 44K C21 H31 N9 O4 S2 c1nc(c2c(n....
7 4OP0 - BT5 C20 H28 N7 O9 P S c1nc(c2c(n....
8 4XU2 Kd = 0.592 nM 44Q C20 H29 N9 O6 S2 c1nc(c2c(n....
9 4XU3 Kd = 0.315 nM 44R C18 H27 N9 O5 S2 c1nc(c2c(n....
10 4XTY Kd = 0.614 nM 44L C20 H28 F N9 O6 S2 c1nc(c2c(n....
11 4XU0 Kd = 0.769 nM 44N C21 H30 N8 O8 S2 C[C@]1([C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 590; Similar ligands found: 19
No: Ligand ECFP6 Tc MDL keys Tc
1 590 1 1
2 594 0.76 0.908163
3 44M 0.751938 0.917526
4 44N 0.669173 0.927835
5 44O 0.62963 0.897959
6 BS5 0.609023 0.876289
7 44L 0.591241 0.841584
8 44Q 0.565217 0.885417
9 BT5 0.55 0.833333
10 44K 0.503497 0.8125
11 BTX 0.5 0.842105
12 44R 0.482269 0.826531
13 649 0.461538 0.885417
14 G5A 0.434109 0.84375
15 8PZ 0.41844 0.84375
16 4YB 0.413793 0.845361
17 SSA 0.410448 0.84375
18 TSB 0.404412 0.822917
19 8X1 0.404412 0.836735
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4XTX; Ligand: 590; Similar sites found with APoc: 315
This union binding pocket(no: 1) in the query (biounit: 4xtx.bio2) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 6GNO XDI None
2 5CLO NS8 None
3 2GTF P1R None
4 1GT4 UNA None
5 4XMF HSM None
6 5O0Z 9GB None
7 3KO0 TFP None
8 1QY1 PRZ None
9 1UQX MMA None
10 6E8I PTR None
11 4WG0 CHD None
12 3FIU POP 0.803213
13 2WLG SOP 0.930233
14 3EHH ADP 1.37615
15 1UJP CIT 1.48148
16 5C9P FUC 1.85185
17 3IAL PR8 1.85185
18 3QSB 743 1.85185
19 2AZ5 307 2.02703
20 2QHS OCA 2.1097
21 4IAW LIZ 2.12766
22 4R38 RBF 2.14286
23 5KHD C2E 2.1978
24 2WKQ FMN 2.22222
25 3ZJX BOG 2.22222
26 5G48 1FL 2.22222
27 4RD0 GDP 2.22222
28 3T4L ZEA 2.22222
29 2IRY DGT 2.22222
30 4UZI IMD 2.22222
31 4TS1 TYR 2.22222
32 2F57 23D 2.22222
33 2ART LPA AMP 2.29008
34 1KGI T4A 2.3622
35 3FJG 3PG 2.39044
36 3TTZ 07N 2.52525
37 2Z3U CRR 2.59259
38 4USF 6UI 2.59259
39 2IU8 PLM 2.59259
40 3BP1 GUN 2.59259
41 2WQN ADP 2.59259
42 4Y4V DAL 2.59259
43 5VNF VAL THR SER VAL VAL 2.59259
44 1H5R THM 2.59259
45 1A5Z FBP 2.59259
46 3QH2 3NM 2.71493
47 5AN1 GSH 2.73973
48 5EJL C2E 2.82258
49 1SJN DUP 2.94118
50 2E5A LAQ 2.96296
51 5LUN OGA 2.96296
52 4X1Z FUC GAL NDG 2.96296
53 6H45 QEI 2.96296
54 5FPN KYD 2.96296
55 5XIO HFG 2.96296
56 1GJW GLC 2.96296
57 3GTD MLI 2.96296
58 4CS4 AXZ 2.96296
59 4PJ3 ANP 2.96296
60 4IDT T28 2.96296
61 5HTX ADP 2.96296
62 1WM1 PTB 2.96296
63 1ZY5 ANP 2.96296
64 5FUS DAO 2.96296
65 2WPB ZZI 2.96296
66 4L50 D8X 3.00752
67 5Z2F PDC 3.01887
68 5J75 6GQ 3.0303
69 3EJ0 11X 3.06122
70 1UKG MMA 3.1746
71 1C3V PDC 3.26531
72 4P83 U5P 3.2967
73 1F9V ADP 3.33333
74 4OE4 NAD 3.33333
75 2OJW ADP 3.33333
76 6F5W KG1 3.33333
77 5WL1 CUY 3.33333
78 5WL1 D3D 3.33333
79 2Z49 AMG 3.33333
80 6BXO SAH 3.33333
81 4IHQ ADP 3.33333
82 3TEG DAH 3.33333
83 2CYB TYR 3.33333
84 2RCU BUJ 3.33333
85 5UE4 5XQ 3.38983
86 5KJW 53C 3.51288
87 3CBC DBS 3.53535
88 4YJK URA 3.57143
89 6G5J EM8 3.63636
90 5D9G GLU ASN LEU TYR PHE GLN 3.65854
91 3IWJ NAD 3.7037
92 1YFS ALA 3.7037
93 5MST AMP 3.7037
94 3B6R ADP 3.7037
95 4KSY 1SY 3.71901
96 1I7M CG 3.74532
97 5TV6 PML 3.75
98 2PR5 FMN 3.78788
99 1GXS DKA 3.79747
100 4DDY DN6 3.80228
101 3NZ1 3NY 3.83142
102 2Z6D FMN 3.84615
103 5HWV MBN 3.84615
104 2Z6C FMN 3.87597
105 3UWB BB2 3.8961
106 4YKI GLY 3.90625
107 3WSG CIT 3.96825
108 4HDK 13X 4
109 5JJU AMP 4.07407
110 4GCZ FMN 4.07407
111 1GPM CIT 4.07407
112 5N9X THR 4.07407
113 6EWZ APC 4.07407
114 4I9B NAD 4.07407
115 1GPM AMP 4.07407
116 3V8S 0HD 4.07407
117 3RSJ NGA GAL SIA 4.07407
118 2BWN SIN 4.07407
119 5H6S HDH 4.07407
120 1CZA GLC 4.07407
121 2V0U FMN 4.10959
122 5DJT FMN 4.13793
123 4QAC KK3 4.14747
124 5O3Q CMP 4.16667
125 5LXT GTP 4.1958
126 4RKX 3S9 4.21456
127 4MOB ADP 4.21687
128 3P7N FMN 4.26357
129 6GG9 FMN 4.32099
130 4NG2 OHN 4.34783
131 4OWK NGA 4.34783
132 2P3I MNA 4.34783
133 4WOE ADP 4.44444
134 1OFL NGK GCD 4.44444
135 1QNR MAB 4.44444
136 3REU ATP 4.44444
137 5VAD PRO 4.44444
138 1X8X TYR 4.44444
139 4C2W ANP 4.44444
140 1NE7 AGP 4.44444
141 5CK5 GDP 4.44444
142 2RC8 DSN 4.44444
143 5KVA SAM 4.44444
144 5A89 FMN 4.48718
145 1RYD GLC 4.65116
146 3QXV MTX 4.7619
147 3A7R LAQ 4.81482
148 1SDW IYT 4.81482
149 5TVF CGQ 4.81482
150 2CZL TLA 4.81482
151 2POC UD1 4.81482
152 4KBA 1QM 4.81482
153 4HWT 1B2 4.81482
154 4YRI 4JH 4.81482
155 3JU6 ANP 4.81482
156 3NEM ATP 4.81482
157 1J71 THR ILE THR SER 4.81482
158 4NS3 NAD 4.81482
159 4G9N NGA 4.8951
160 4R29 SAM 4.91071
161 5DJU FMN 4.91803
162 2AGC DAO 4.93827
163 3IT6 ORN 5.02513
164 2CBZ ATP 5.06329
165 5F90 GLA GAL BGC 5VQ 5.12821
166 1E1O LYS 5.18518
167 5YSZ CBI 5.18518
168 5USZ SKE 5.18518
169 2HK9 ATR 5.18518
170 4EES FMN 5.21739
171 5AHW CMP 5.44218
172 1SBR VIB 5.5
173 5L2R MLA 5.55556
174 5YJS SAL 5.55556
175 3T1A 5MA 5.55556
176 2VGK REZ 5.55556
177 1LSH PLD 5.55556
178 3ICS ADP 5.55556
179 1U6R ADP 5.55556
180 4BG4 ADP 5.55556
181 3KYF 5GP 5GP 5.62771
182 3KIF GDL 5.66038
183 3DUV KDO 5.72519
184 4RYV ZEA 5.80645
185 2G30 ALA ALA PHE 5.81395
186 3GD8 GOL 5.8296
187 1PVC ILE SER GLU VAL 5.88235
188 1VJ7 GPX 5.92593
189 1VRP ADP 5.92593
190 3AB4 THR 5.92593
191 3NB0 G6P 5.92593
192 3A75 GLU 5.92593
193 2HJ4 PNZ 5.92593
194 5NXX 3Q7 5.97015
195 5DKK FMN 6.2069
196 2RDE C2E 6.2963
197 3G1Z AMP 6.2963
198 2I4O ATP 6.2963
199 3KYG 5GP 5GP 6.2963
200 4RF7 ARG 6.2963
201 3A5Z KAA 6.2963
202 2NV2 GLN 6.2963
203 1LVW TYD 6.2963
204 2YVJ NAI 6.2963
205 3TK1 GDP 6.2963
206 3A5Y KAA 6.2963
207 1F5F DHT 6.34146
208 1B4P GPS 6.45161
209 1W8S FBP 6.46388
210 4J0Q GDP 6.46651
211 2YKL NLD 6.60377
212 2QHV OC9 6.66667
213 5MRH Q9Z 6.66667
214 3VGL BGC 6.66667
215 4QS9 BGC 6.66667
216 3DEF GDP 6.66667
217 3MF2 AMP 6.66667
218 3WLV AZA 6.73077
219 5M6N 7H9 6.77966
220 4LO2 GAL BGC 6.80272
221 4HIA FMN 6.81818
222 3SAO DBH 6.875
223 5OCG 9R5 6.87831
224 3T50 FMN 7.03125
225 2I56 RNS 7.03704
226 4RUS NAG 7.14286
227 4RUS NDG 7.14286
228 5EYW PGA 7.22892
229 1N9L FMN 7.33945
230 2QPU QPU 7.40741
231 2QPU QPS 7.40741
232 5C03 AGS 7.40741
233 1RV0 NDG 7.5
234 6FA4 D1W 7.51445
235 1B7A OPE 7.52688
236 2J9D ADP 7.56302
237 5F6U 5VK 7.64331
238 4H2X G5A 7.76699
239 1TIQ COA 7.77778
240 1BW9 NAD 7.77778
241 1RQH PYR 7.77778
242 3KVY URA 7.77778
243 3L9W AMP 7.77778
244 4CR6 MAN 7.77778
245 3LF0 ATP 7.89474
246 5UKL SIX 8.06452
247 3E9I XAH 8.14815
248 5EFW FMN 8.33333
249 1UYY BGC BGC 8.39695
250 3NCQ ATP 8.40336
251 4USI ATP 8.44156
252 4FE2 AIR 8.51852
253 1T5C ADP 8.51852
254 3A76 SPD 8.52273
255 5TBM 79A 8.54701
256 3UW4 MAA CHG PRO 0DQ 8.69565
257 1UBY DMA 8.88889
258 5XLY C2E 8.88889
259 1T5B FMN 8.95522
260 3K56 IS3 9.02256
261 3ACL 3F1 9.12162
262 3CM2 X23 9.23077
263 3K1X DBX 9.23077
264 1UJ5 5RP 9.2511
265 5CPR 539 9.32836
266 4WUJ FMN 9.52381
267 3WXL ADP 9.62963
268 1HE1 AF3 9.65909
269 4GDX GLU 9.74359
270 3KFF ZBT 9.87654
271 3KFF XBT 9.87654
272 2WME NAP 10
273 2J3M PRI 10
274 5N5U 7N8 10
275 2J3M ATP 10
276 1S17 GNR 10
277 5SVV FMN 10.219
278 6GBV FMN 10.274
279 5Y4R C2E 10.3448
280 1VL1 CIT 10.3448
281 5DYO FLU 10.3774
282 4IEN GDP 10.4294
283 2CE7 ADP 10.7407
284 3U6B GDP 10.7407
285 4P3Y GDP 10.7407
286 2HCJ GDP 10.7407
287 3HQP ATP 10.7407
288 1OW3 GDP 10.8808
289 5C83 4YN 10.9091
290 1GRN AF3 10.9948
291 1G51 AMP 11.1111
292 1KK1 GNP 11.1111
293 4K55 H6P 11.2903
294 5IRC GDP 11.2903
295 5T8U LPA 11.4815
296 2GQS C2R 11.8143
297 3O8M BGC 11.8519
298 3O8M GLC 11.8519
299 4SGA ACE PRO ALA PRO PHE 12.1547
300 2PNC CLU 12.2222
301 1VBO MAN MAN MAN 12.7517
302 3IWD M2T 12.9032
303 1A0J BEN 13.4529
304 2CJU PHX 14.0496
305 3VPB GLU 14.2857
306 4RT1 C2E 14.2857
307 5BSH PRO 14.8148
308 3H0L ADP 14.8936
309 2DC1 CIT 15.2542
310 1V3S ATP 16.3793
311 5FUI APY 16.6667
312 3UW5 MAA CHG PRO 0DQ 24.1379
313 5XG5 A2G 24.8276
314 1LNX URI 25.9259
315 3RF4 FUN 28.4483
Pocket No.: 2; Query (leader) PDB : 4XTX; Ligand: 590; Similar sites found with APoc: 88
This union binding pocket(no: 2) in the query (biounit: 4xtx.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 5N2D 8J8 None
3 2ZX2 RAM None
4 1VAY AZA 1.85185
5 3TUR 6CL 2.22222
6 3BRE C2E 2.22222
7 5X7Q GLC GLC 2.59259
8 1T9D PYD 2.59259
9 2JGV ADP 2.59259
10 1H5R G1P 2.59259
11 4CS4 ANP 2.96296
12 5TUF TDC 2.96296
13 3MVH WFE 2.96296
14 4AG5 ADP 2.96296
15 3VKX T3 3.06513
16 3OQJ 3CX 3.11284
17 1Q8V MAN MAN 3.1746
18 2GND MAN 3.1746
19 5HCA BGC 3.33333
20 4F8L AES 3.44828
21 1Y7P RIP 3.58744
22 5EW9 5VC 3.7037
23 1PVS 7HP 3.7037
24 1WDK N8E 3.7037
25 5LHT TIH 3.7037
26 1KQR MNA 3.91061
27 5M37 9SZ 3.91304
28 1CZA G6P 4.07407
29 3FSY SCA 4.07407
30 2OHH FMN 4.07407
31 4WXJ GLU 4.08922
32 4B0T ADP 4.25963
33 1CT9 GLN 4.44444
34 5HY1 WDL 4.44444
35 2P0D I3P 4.65116
36 1ULE GLA GAL NAG 4.66667
37 5W75 SUC 4.81482
38 4MZU TDR 4.81482
39 2J9L ATP 4.86486
40 2BKX F6R 4.95868
41 4WCX MET 5.18518
42 2CHT TSA 5.51181
43 2YLN CYS 5.55556
44 3DLG GWE 5.55556
45 4FBL SPD 5.55556
46 1KC7 PPR 5.55556
47 1OFZ FUC 5.55556
48 1QKQ MAN 5.6338
49 5TZO 7V7 5.92593
50 2HZL PYR 5.92593
51 1J2Z SOG 5.92593
52 3M6P BB2 6.21762
53 4TQK NAG 6.2963
54 5CIC 51R 6.48148
55 2PFC PLM 6.55738
56 2JBH 5GP 6.66667
57 1H65 GDP 6.66667
58 1DAR GDP 6.66667
59 4YMZ 13P 6.77291
60 2AF6 BRU 6.97674
61 2VL1 GLY GLY 7.03704
62 4L3L 5FI 7.03704
63 6FRN FMN 7.03704
64 5CGE 51F 7.40741
65 3C8E GSH 7.40741
66 1RVX SIA GAL NAG 7.5
67 2W58 ADP 7.92079
68 2WJG GDP 7.97872
69 2WCU FUC 8.05369
70 6DXS HJ7 8.88889
71 5IFS ADP 8.88889
72 4IF4 BEF 9.13461
73 3A16 PXO 10.3704
74 3HQP OXL 10.7407
75 3HQP FDP 10.7407
76 5DQW ADP 11.8483
77 3RLF MAL 12.5926
78 1B4B ARG 12.6761
79 1VBO MAN 12.7517
80 5VM6 9EG 13.1387
81 5E62 Z3Q GAL 5N6 13.3333
82 5L8L ADP 13.6752
83 2JK0 ASP 13.7037
84 1XKV ATP 13.7037
85 1MFI FHC 14.0351
86 6HKE LMR 16.2963
87 3JQM GTP 21.6561
88 2XN5 FUN 34.2857
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