Receptor
PDB id Resolution Class Description Source Keywords
5CHR 1.98 Å EC: 1.11.1.7 DEHALOPEROXIDASE B IN COMPLEX WITH SUBSTRATE P-NITROCATECHOL AMPHITRITE ORNATA SUBSTRATE OXIDOREDUCTASE
Ref.: NONMICROBIAL NITROPHENOL DEGRADATION VIA PEROXYGENA ACTIVITY OF DEHALOPEROXIDASE-HEMOGLOBIN FROM AMPHIT ORNATA. BIOCHEMISTRY V. 55 2465 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HEM A:201;
B:201;
Part of Protein;
Part of Protein;
none;
none;
submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
GOL B:203;
A:206;
A:207;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
4NC B:202;
A:204;
Valid;
Valid;
none;
none;
Kd = 40 uM
155.108 C6 H5 N O4 c1cc(...
OXY A:205;
Invalid;
none;
submit data
31.999 O2 O=O
SO4 A:203;
A:202;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5CHR 1.98 Å EC: 1.11.1.7 DEHALOPEROXIDASE B IN COMPLEX WITH SUBSTRATE P-NITROCATECHOL AMPHITRITE ORNATA SUBSTRATE OXIDOREDUCTASE
Ref.: NONMICROBIAL NITROPHENOL DEGRADATION VIA PEROXYGENA ACTIVITY OF DEHALOPEROXIDASE-HEMOGLOBIN FROM AMPHIT ORNATA. BIOCHEMISTRY V. 55 2465 2016
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3LB3 Kd = 1.78 mM 4CH C6 H5 Cl O c1cc(ccc1O....
2 3LB1 Kd = 0.536 mM IOL C6 H5 I O c1cc(ccc1O....
3 4KMV - T6C C6 H3 Cl3 O c1c(cc(c(c....
4 4FH7 Ki = 0.51 mM TBP C6 H3 Br3 O c1c(cc(c(c....
5 4FH6 - TBP C6 H3 Br3 O c1c(cc(c(c....
6 4KMW - T6C C6 H3 Cl3 O c1c(cc(c(c....
7 3LB2 Kd = 1.15 mM BML C6 H5 Br O c1cc(ccc1O....
8 4HSX - BML C6 H5 Br O c1cc(ccc1O....
9 5CHR Kd = 40 uM 4NC C6 H5 N O4 c1cc(c(cc1....
10 4ILZ - TBP C6 H3 Br3 O c1c(cc(c(c....
11 4KN3 - T6C C6 H3 Cl3 O c1c(cc(c(c....
12 5CHQ Kd = 262 uM NPO C6 H5 N O3 c1cc(ccc1[....
13 3LB4 Kd = 3.72 mM FPN C6 H5 F O c1cc(ccc1O....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3LB3 Kd = 1.78 mM 4CH C6 H5 Cl O c1cc(ccc1O....
2 3LB1 Kd = 0.536 mM IOL C6 H5 I O c1cc(ccc1O....
3 4KMV - T6C C6 H3 Cl3 O c1c(cc(c(c....
4 4FH7 Ki = 0.51 mM TBP C6 H3 Br3 O c1c(cc(c(c....
5 4FH6 - TBP C6 H3 Br3 O c1c(cc(c(c....
6 4KMW - T6C C6 H3 Cl3 O c1c(cc(c(c....
7 3LB2 Kd = 1.15 mM BML C6 H5 Br O c1cc(ccc1O....
8 4HSX - BML C6 H5 Br O c1cc(ccc1O....
9 5CHR Kd = 40 uM 4NC C6 H5 N O4 c1cc(c(cc1....
10 4ILZ - TBP C6 H3 Br3 O c1c(cc(c(c....
11 4KN3 - T6C C6 H3 Cl3 O c1c(cc(c(c....
12 5CHQ Kd = 262 uM NPO C6 H5 N O3 c1cc(ccc1[....
13 3LB4 Kd = 3.72 mM FPN C6 H5 F O c1cc(ccc1O....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3LB3 Kd = 1.78 mM 4CH C6 H5 Cl O c1cc(ccc1O....
2 3LB1 Kd = 0.536 mM IOL C6 H5 I O c1cc(ccc1O....
3 4KMV - T6C C6 H3 Cl3 O c1c(cc(c(c....
4 4FH7 Ki = 0.51 mM TBP C6 H3 Br3 O c1c(cc(c(c....
5 4FH6 - TBP C6 H3 Br3 O c1c(cc(c(c....
6 4KMW - T6C C6 H3 Cl3 O c1c(cc(c(c....
7 3LB2 Kd = 1.15 mM BML C6 H5 Br O c1cc(ccc1O....
8 4HSX - BML C6 H5 Br O c1cc(ccc1O....
9 5CHR Kd = 40 uM 4NC C6 H5 N O4 c1cc(c(cc1....
10 4ILZ - TBP C6 H3 Br3 O c1c(cc(c(c....
11 4KN3 - T6C C6 H3 Cl3 O c1c(cc(c(c....
12 5CHQ Kd = 262 uM NPO C6 H5 N O3 c1cc(ccc1[....
13 3LB4 Kd = 3.72 mM FPN C6 H5 F O c1cc(ccc1O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4NC; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 4NC 1 1
2 DNF 0.527778 0.772727
3 P9P 0.527778 0.785714
4 CSN 0.44186 0.698113
5 NPO 0.411765 0.815789
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CHR; Ligand: 4NC; Similar sites found: 195
This union binding pocket(no: 1) in the query (biounit: 5chr.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4RHP PEF 0.000391 0.49246 None
2 5V4R MGT 0.001085 0.46205 None
3 1L6O SER LEU LYS LEU MET THR THR VAL 0.002347 0.45228 None
4 4ZOM 4Q3 0.02086 0.4517 None
5 4IEH 1E9 0.004447 0.44922 None
6 4P3H 25G 0.008133 0.43478 None
7 5G3N X28 0.007374 0.43379 None
8 5LJ0 6XX 0.009037 0.43315 None
9 2VWA PTY 0.003516 0.43269 None
10 5N8V KZZ 0.004132 0.42883 None
11 5HGZ ACO 0.02131 0.41484 None
12 4V24 GYR 0.03029 0.41361 None
13 5N7O 69Y 0.01444 0.4131 None
14 3RG9 WRA 0.04726 0.40949 None
15 2GJ3 FAD 0.01972 0.40855 None
16 5KAU RHQ 0.01914 0.40831 None
17 3EWK FAD 0.0199 0.40796 None
18 4EKQ NPO 0.01946 0.40699 None
19 2HW2 RFP 0.0272 0.40609 None
20 3L1N PLM 0.01297 0.40288 None
21 1CMC SAM 0.04077 0.40243 None
22 1Q3A NGH 0.01933 0.40215 None
23 2ALG HP6 0.0318 0.4003 None
24 2ALG DAO 0.0318 0.4003 None
25 5OCA 9QZ 0.001043 0.45115 2.18978
26 3V49 PK0 0.006528 0.44175 2.18978
27 1YOK P6L 0.01518 0.43546 2.18978
28 1YUC EPH 0.009235 0.43455 2.18978
29 4RPL 3UC 0.03866 0.43424 2.18978
30 5NTW 98N 0.02178 0.42155 2.18978
31 3KC1 2T6 0.01863 0.4094 2.18978
32 1RV1 IMZ 0.01018 0.41586 2.35294
33 3SVJ 4LI 0.004263 0.44567 2.91971
34 1HN4 MJI 0.04448 0.42775 3.05344
35 3TGE TGE 0.00344 0.48469 3.64964
36 4ORM 2V6 0.007663 0.47077 3.64964
37 4ORM ORO 0.007663 0.47077 3.64964
38 4ORM FMN 0.007663 0.47077 3.64964
39 4UWJ 7L5 0.01341 0.45665 3.64964
40 4UWJ MYA 0.01341 0.45665 3.64964
41 3ET3 ET1 0.003066 0.45243 3.64964
42 5DCH 1YO 0.002162 0.43681 3.64964
43 1GHE ACO 0.01023 0.43085 3.64964
44 2WCJ M21 0.01168 0.4262 3.64964
45 5L7G 6QE 0.01559 0.41998 3.64964
46 2FDW D3G 0.003715 0.40847 3.64964
47 3G9E RO7 0.04709 0.40478 3.64964
48 3RGA ILD 0.03338 0.40376 3.64964
49 1VPV PLM 0.03776 0.40129 3.64964
50 5F1R 42O 0.000317 0.51315 4.37956
51 3L9R L9R 0.003546 0.46647 4.37956
52 1SO2 666 0.002009 0.45495 4.37956
53 5WRE 7TL 0.004787 0.44396 4.37956
54 4DR9 BB2 0.003645 0.4423 4.37956
55 4P6X HCY 0.006994 0.43433 4.37956
56 5CSD ACD 0.01645 0.43245 4.37956
57 3L9R L9Q 0.01509 0.43182 4.37956
58 1SR7 MOF 0.01811 0.42647 4.37956
59 4QOM PYG 0.01001 0.42559 4.37956
60 3Q8G PEE 0.03715 0.42529 4.37956
61 2J8C SPO 0.04934 0.42522 4.37956
62 2J8C U10 0.04934 0.42522 4.37956
63 3GN8 DEX 0.01233 0.42196 4.37956
64 4CA5 3EF 0.04203 0.42018 4.37956
65 4LSJ LSJ 0.01416 0.42009 4.37956
66 2YNC YNC 0.02979 0.41914 4.37956
67 4OAR 2S0 0.01605 0.41593 4.37956
68 3BQD DAY 0.01782 0.41484 4.37956
69 1NP7 FAD 0.02773 0.41342 4.37956
70 4JE7 BB2 0.01838 0.41002 4.37956
71 1LOX RS7 0.01901 0.40596 4.37956
72 1TO9 HMH 0.006349 0.4039 4.37956
73 5JO1 6LM 0.02903 0.40107 4.37956
74 3T03 3T0 0.01977 0.40384 4.92958
75 4RC8 STE 0.001789 0.46713 5.10949
76 3ICS COA 0.005971 0.45245 5.10949
77 4KCF AKM 0.005956 0.4423 5.10949
78 5AZC PGT 0.03812 0.43791 5.10949
79 3Q2H QHF 0.01312 0.41557 5.10949
80 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.02302 0.4099 5.10949
81 1JF0 CZH 0.03357 0.40425 5.10949
82 4JGX PLM 0.009281 0.41845 5.42636
83 1UVC STE 0.03474 0.40685 5.49451
84 3E8T UQ8 0.00562 0.47217 5.83942
85 5UGW GSH 0.002206 0.43992 5.83942
86 2C78 PUL 0.02639 0.43716 5.83942
87 4E90 7RG 0.006251 0.43381 5.83942
88 3QKD HI0 0.01077 0.43014 5.83942
89 4Y2H SAH 0.02276 0.42847 5.83942
90 1IYK MYA 0.01698 0.42696 5.83942
91 4Y2H 49K 0.02634 0.42501 5.83942
92 4QGE 35O 0.01158 0.41614 5.83942
93 3MBG FAD 0.02341 0.41366 5.83942
94 1YKD CMP 0.01518 0.41113 5.83942
95 1LSH PLD 0.0437 0.40098 5.83942
96 3N7S 3N7 0.0125 0.41005 6.08696
97 5IR4 ZPE 0.006181 0.46195 6.56934
98 4DE9 VTP 0.005106 0.45499 6.56934
99 1IID NHM 0.008316 0.45207 6.56934
100 3WYJ H78 0.03144 0.43437 6.56934
101 4MNS 2AX 0.02645 0.43089 6.56934
102 2QYK NPV 0.004847 0.42579 6.56934
103 1U3D FAD 0.01764 0.42312 6.56934
104 3JRS A8S 0.009002 0.423 6.56934
105 4COL DTP 0.01383 0.4121 6.56934
106 3KDJ A8S 0.01849 0.40998 6.56934
107 3CGD NAD 0.01921 0.45483 7.29927
108 3CGD FAD 0.01921 0.45483 7.29927
109 3CGD COA 0.01921 0.45483 7.29927
110 5EW9 5VC 0.04141 0.44183 7.29927
111 1ATL 0QI 0.01545 0.41889 7.29927
112 5EY0 GTP 0.01403 0.40642 7.29927
113 5LX9 OLB 0.0008798 0.40382 7.29927
114 2D5Z L35 0.04473 0.43307 8.0292
115 4B7P 9UN 0.03466 0.42342 8.0292
116 4RI1 ACO 0.01692 0.41439 8.0292
117 4OIC A8S 0.01545 0.41058 8.0292
118 4UCC ZKW 0.008965 0.40356 8.0292
119 3G4G D71 0.0002712 0.50382 8.75912
120 1YQZ FAD 0.01015 0.4635 8.75912
121 3ET1 ET1 0.002357 0.4556 8.75912
122 3KDU NKS 0.01079 0.45286 8.75912
123 3G58 988 0.0002186 0.44709 8.75912
124 5IF4 6AK 0.007602 0.44359 8.75912
125 4PYW ACE THR THR ALA ILE NH2 0.007761 0.43719 8.75912
126 1LN1 DLP 0.01694 0.42812 8.75912
127 2UW1 GVM 0.003473 0.41704 8.75912
128 1M13 HYF 0.02681 0.41626 8.75912
129 4V3I ASP LEU THR ARG PRO 0.005738 0.41274 8.75912
130 3GFZ FMN 0.01753 0.40319 8.75912
131 1NRL SRL 0.02585 0.40253 8.75912
132 5UC9 MYR 0.01264 0.40072 8.75912
133 2FP2 TSA 0.001012 0.47459 9.48905
134 5TO8 7FM 0.01624 0.43582 9.48905
135 2ZXG S23 0.03393 0.40418 9.48905
136 1XMY ROL 0.0002316 0.49043 10.219
137 1XVB BHL 0.0017 0.48829 10.219
138 3GWT 066 0.00143 0.48499 10.219
139 5B4B LP5 0.003578 0.46043 10.219
140 1R5L VIV 0.004201 0.45247 10.219
141 3NTD COA 0.006848 0.45165 10.219
142 3H0A D30 0.005431 0.44813 10.219
143 5C1M 4VO 0.002732 0.44394 10.219
144 2C43 COA 0.005751 0.44275 10.219
145 1XM4 PIL 0.0004597 0.43273 10.219
146 1XMU ROF 0.0003492 0.42845 10.219
147 5C1M CLR 0.004788 0.42118 10.219
148 1XVB 3BR 0.009668 0.41557 10.219
149 2FV5 541 0.02726 0.41497 10.219
150 1KUK PCA LYS TRP 0.01476 0.40787 10.219
151 3IX8 TX3 0.03714 0.40269 10.219
152 5V3Y 5V8 0.003489 0.43673 10.9489
153 4GFD 0YB 0.02078 0.41079 10.9489
154 1FO0 ILE ASN PHE ASP PHE ASN THR ILE 0.0323 0.41974 11.6071
155 4BNU 9KQ 0.001487 0.47326 11.6788
156 4U0S ADP 0.02322 0.4001 11.6788
157 5MWE TCE 0.006253 0.41887 12.3457
158 4OMJ 2TX 0.006657 0.45141 12.4088
159 2PX6 DH9 0.003529 0.4435 12.4088
160 5K52 OCD 0.005107 0.44094 12.4088
161 3R9V DXC 0.006382 0.41465 12.4088
162 2A1L PCW 0.001912 0.49175 13.1387
163 5U98 1KX 0.00692 0.47139 13.1387
164 2Z7I 742 0.02264 0.4456 13.1387
165 5U98 VAL THR THR ASP ILE GLN VAL LYS VAL 0.01303 0.43341 13.1387
166 3OV6 MK0 0.0246 0.41629 13.1387
167 1GNI OLA 0.03007 0.47074 13.8686
168 1P0H ACO 0.02431 0.44231 13.8686
169 3TJH SER PRO LEU ASP SER LEU TRP TRP ILE 0.0261 0.42579 13.8686
170 2ZFZ ARG 0.02194 0.4325 13.9241
171 3G08 FEE 0.00057 0.52929 14.5985
172 3SCM LGN 0.004307 0.47803 14.5985
173 2ZCQ B65 0.006243 0.46267 14.5985
174 4ZW3 4S9 0.01803 0.42877 15.3285
175 4TV1 36M 0.01059 0.40843 15.3285
176 1BWO LPC 0.009606 0.42432 15.5556
177 4XIZ LPP 0.03536 0.41058 15.7143
178 1W96 S1A 0.01175 0.41751 16.0584
179 1J78 OLA 0.006637 0.41732 16.0584
180 1J78 VDY 0.003954 0.40568 16.0584
181 4ZBR DIF 0.002456 0.47499 16.7883
182 4ZBR NPS 0.002324 0.47499 16.7883
183 4H6Q TFB 0.01032 0.43591 17.5182
184 1RX0 2MC 0.03356 0.40255 17.5182
185 2DYR PGV 0.003632 0.47016 18.3673
186 2DYR TGL 0.01957 0.42562 18.3673
187 3WCA FPS 0.0094 0.43917 18.9781
188 5L2J 6UL 0.02151 0.44432 20.438
189 5L2J 70E 0.02254 0.44432 20.438
190 5MW4 5JU 0.03098 0.42325 21.1679
191 4WZ8 3W7 0.04903 0.40888 21.1679
192 4QWT ACD 0.006143 0.44415 21.8978
193 2O1V ADP 0.004566 0.43035 22.6277
194 3RLF MAL 0.01223 0.40701 26.2774
195 2O5L MNR 0.01847 0.40556 26.2774
Pocket No.: 2; Query (leader) PDB : 5CHR; Ligand: 4NC; Similar sites found: 25
This union binding pocket(no: 2) in the query (biounit: 5chr.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U72 MTX 0.02489 0.42538 None
2 1U72 NDP 0.02489 0.42538 None
3 1I1D 16G 0.01535 0.4189 None
4 1I1D COA 0.01129 0.4161 None
5 4DO1 ANN 0.02097 0.40023 1.45985
6 2IDO TMP 0.01225 0.40796 2.91971
7 3ZJQ NCA 0.01111 0.43103 4.37956
8 3SQP 3J8 0.005139 0.42012 4.37956
9 3GGO NAI 0.02716 0.41621 4.37956
10 3GGO ENO 0.02716 0.41621 4.37956
11 1Q2C COA 0.02158 0.40063 5.83942
12 3NRR D16 0.008312 0.44771 6.56934
13 3NRR NAP 0.03309 0.41252 6.56934
14 1YQS BSA 0.03058 0.4058 6.56934
15 3TDC 0EU 0.00002637 0.54549 7.29927
16 2WHP HI6 0.01075 0.40579 7.29927
17 3WV1 WHH 0.04488 0.40462 8.0292
18 1YMT DR9 0.01203 0.42049 8.94309
19 3FUR Z12 0.03986 0.40983 10.219
20 2ZMF CMP 0.01292 0.40648 10.219
21 2Q2Y MKR 0.03803 0.40487 11.6788
22 2Q2Y ADP 0.03961 0.40487 11.6788
23 4QJR PIZ 0.01621 0.41125 13.8686
24 2Y69 CHD 0.01231 0.40356 14.2857
25 2QE4 JJ3 0.02329 0.4262 15.3285
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