Receptor
PDB id Resolution Class Description Source Keywords
2Y6F 1.79 Å EC: 1.21.3.1 ISOPENICILLIN N SYNTHASE WITH AC-D-S-METHYL-3R-METHYLCYSTEIN EMERICELLA NIDULANS OXIDOREDUCTASE OXYGENASE PENICILLIN BIOSYNTHESIS
Ref.: ISOPENICILLIN N SYNTHASE BINDS DELTA-(L-ALPHA-AMINOADIPOYL) -L-CYSTEINYL-D-THIA-ALLO-ISOLEUCINE THROUGH BOTH SU ATOMS. CHEMBIOCHEM V. 12 1881 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE A:1333;
Part of Protein;
none;
submit data
55.845 Fe [Fe+3...
M9F A:1332;
Valid;
none;
submit data
395.495 C14 H25 N3 O6 S2 CC([C...
SO4 A:1334;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1ODM 1.15 Å EC: 1.21.3.1 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ANAEROBI VINYLGLYCINE FE COMPLEX) EMERICELLA NIDULANS ANTIBIOTIC BIOSYNTHESIS B-LACTAM ANTIBIOTIC OXYGENASE PENBIOSYNTHESIS OXIDOREDUCTASE IRON
Ref.: CRYSTALLOGRAPHIC STUDIES ON THE REACTION OF ISOPENI SYNTHASE WITH AN UNSATURATED SUBSTRATE ANALOGUE ORG.BIOMOL.CHEM. V. 1 1455 2003
Members (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3ZKY - WT4 C14 H25 N3 O6 S2 CSC[C@H](C....
2 2Y6F - M9F C14 H25 N3 O6 S2 CC([C@H](C....
3 1HB2 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
4 1ODN - APV C13 H19 N3 O7 S C(C[C@@H](....
5 2VBB - VAZ C13 H22 N2 O9 S2 CS[C@@H]([....
6 3ZKU - HCV C15 H27 N3 O6 S CC(C)[C@H]....
7 2VBP - VB1 C13 H23 N3 O6 S CC[C@@H](C....
8 4BB3 - KKA C10 H18 N2 O5 S C(C[C@@H](....
9 1QJE - IP1 C14 H21 N3 O6 S CC1([C@@H]....
10 1HB4 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
11 2BU9 - HFV C14 H19 F6 N3 O6 S C(C[C@@H](....
12 1W06 - W05 C12 H21 N3 O6 S C[C@H](C(=....
13 1OC1 - ASV C13 H21 N3 O6 S C=C[C@H](C....
14 1HB1 - OCV C14 H24 N2 O7 S CC(C)[C@H]....
15 2IVJ - BCV C14 H23 N3 O6 S C1CC1[C@H]....
16 2JB4 - A14 C15 H22 N2 O6 S CC1([C@@H]....
17 2VCM - M11 C15 H26 N2 O7 S CC(C)[C@H]....
18 1W04 - HCG C11 H19 N3 O6 S C(C[C@@H](....
19 1W3X - W2X C15 H24 N2 O8 S C[C@H](CO)....
20 1HB3 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
21 1ODM - ASV C13 H21 N3 O6 S C=C[C@H](C....
22 2Y60 - M8F C14 H25 N3 O6 S2 CSCC[C@H](....
23 1W3V - MDZ C15 H26 N2 O7 S CC(C)[C@H]....
24 1QJF - ACS C13 H21 N3 O7 S2 C[S@](=O)C....
25 1UZW - CDH C14 H23 N3 O6 S CC(=C)[C@H....
26 2IVI - ACW C15 H25 N3 O6 S CC1(CC1)[C....
27 2VAU - V20 C13 H22 N2 O7 S2 CSC[C@H](C....
28 1W03 - HCG C11 H19 N3 O6 S C(C[C@@H](....
29 1BK0 - ACV C14 H25 N3 O6 S CC(C)[C@H]....
30 1OBN - ASV C13 H21 N3 O6 S C=C[C@H](C....
31 3ZOI - M2W C14 H25 N3 O7 S C[C@@H]([C....
32 2VBD - V10 C13 H22 N2 O7 S2 CSC[C@@H](....
33 1W05 - W05 C12 H21 N3 O6 S C[C@H](C(=....
34 2WO7 - ASV C13 H21 N3 O6 S C=C[C@H](C....
35 1QIQ - ACC C13 H24 N3 O6 S2 CSC[C@H](C....
36 1BLZ - ACV C14 H25 N3 O6 S CC(C)[C@H]....
70% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3ZKY - WT4 C14 H25 N3 O6 S2 CSC[C@H](C....
2 2Y6F - M9F C14 H25 N3 O6 S2 CC([C@H](C....
3 1HB2 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
4 1ODN - APV C13 H19 N3 O7 S C(C[C@@H](....
5 2VBB - VAZ C13 H22 N2 O9 S2 CS[C@@H]([....
6 3ZKU - HCV C15 H27 N3 O6 S CC(C)[C@H]....
7 2VBP - VB1 C13 H23 N3 O6 S CC[C@@H](C....
8 4BB3 - KKA C10 H18 N2 O5 S C(C[C@@H](....
9 1QJE - IP1 C14 H21 N3 O6 S CC1([C@@H]....
10 1HB4 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
11 2BU9 - HFV C14 H19 F6 N3 O6 S C(C[C@@H](....
12 1W06 - W05 C12 H21 N3 O6 S C[C@H](C(=....
13 1OC1 - ASV C13 H21 N3 O6 S C=C[C@H](C....
14 1HB1 - OCV C14 H24 N2 O7 S CC(C)[C@H]....
15 2IVJ - BCV C14 H23 N3 O6 S C1CC1[C@H]....
16 2JB4 - A14 C15 H22 N2 O6 S CC1([C@@H]....
17 2VCM - M11 C15 H26 N2 O7 S CC(C)[C@H]....
18 1W04 - HCG C11 H19 N3 O6 S C(C[C@@H](....
19 1W3X - W2X C15 H24 N2 O8 S C[C@H](CO)....
20 1HB3 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
21 1ODM - ASV C13 H21 N3 O6 S C=C[C@H](C....
22 2Y60 - M8F C14 H25 N3 O6 S2 CSCC[C@H](....
23 1W3V - MDZ C15 H26 N2 O7 S CC(C)[C@H]....
24 1QJF - ACS C13 H21 N3 O7 S2 C[S@](=O)C....
25 1UZW - CDH C14 H23 N3 O6 S CC(=C)[C@H....
26 2IVI - ACW C15 H25 N3 O6 S CC1(CC1)[C....
27 2VAU - V20 C13 H22 N2 O7 S2 CSC[C@H](C....
28 1W03 - HCG C11 H19 N3 O6 S C(C[C@@H](....
29 1BK0 - ACV C14 H25 N3 O6 S CC(C)[C@H]....
30 1OBN - ASV C13 H21 N3 O6 S C=C[C@H](C....
31 3ZOI - M2W C14 H25 N3 O7 S C[C@@H]([C....
32 2VBD - V10 C13 H22 N2 O7 S2 CSC[C@@H](....
33 1W05 - W05 C12 H21 N3 O6 S C[C@H](C(=....
34 2WO7 - ASV C13 H21 N3 O6 S C=C[C@H](C....
35 1QIQ - ACC C13 H24 N3 O6 S2 CSC[C@H](C....
36 1BLZ - ACV C14 H25 N3 O6 S CC(C)[C@H]....
50% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3ZKY - WT4 C14 H25 N3 O6 S2 CSC[C@H](C....
2 2Y6F - M9F C14 H25 N3 O6 S2 CC([C@H](C....
3 1HB2 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
4 1ODN - APV C13 H19 N3 O7 S C(C[C@@H](....
5 2VBB - VAZ C13 H22 N2 O9 S2 CS[C@@H]([....
6 3ZKU - HCV C15 H27 N3 O6 S CC(C)[C@H]....
7 2VBP - VB1 C13 H23 N3 O6 S CC[C@@H](C....
8 4BB3 - KKA C10 H18 N2 O5 S C(C[C@@H](....
9 1QJE - IP1 C14 H21 N3 O6 S CC1([C@@H]....
10 1HB4 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
11 2BU9 - HFV C14 H19 F6 N3 O6 S C(C[C@@H](....
12 1W06 - W05 C12 H21 N3 O6 S C[C@H](C(=....
13 1OC1 - ASV C13 H21 N3 O6 S C=C[C@H](C....
14 1HB1 - OCV C14 H24 N2 O7 S CC(C)[C@H]....
15 2IVJ - BCV C14 H23 N3 O6 S C1CC1[C@H]....
16 2JB4 - A14 C15 H22 N2 O6 S CC1([C@@H]....
17 2VCM - M11 C15 H26 N2 O7 S CC(C)[C@H]....
18 1W04 - HCG C11 H19 N3 O6 S C(C[C@@H](....
19 1W3X - W2X C15 H24 N2 O8 S C[C@H](CO)....
20 1HB3 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
21 1ODM - ASV C13 H21 N3 O6 S C=C[C@H](C....
22 2Y60 - M8F C14 H25 N3 O6 S2 CSCC[C@H](....
23 1W3V - MDZ C15 H26 N2 O7 S CC(C)[C@H]....
24 1QJF - ACS C13 H21 N3 O7 S2 C[S@](=O)C....
25 1UZW - CDH C14 H23 N3 O6 S CC(=C)[C@H....
26 2IVI - ACW C15 H25 N3 O6 S CC1(CC1)[C....
27 2VAU - V20 C13 H22 N2 O7 S2 CSC[C@H](C....
28 1W03 - HCG C11 H19 N3 O6 S C(C[C@@H](....
29 1BK0 - ACV C14 H25 N3 O6 S CC(C)[C@H]....
30 1OBN - ASV C13 H21 N3 O6 S C=C[C@H](C....
31 3ZOI - M2W C14 H25 N3 O7 S C[C@@H]([C....
32 2VBD - V10 C13 H22 N2 O7 S2 CSC[C@@H](....
33 1W05 - W05 C12 H21 N3 O6 S C[C@H](C(=....
34 2WO7 - ASV C13 H21 N3 O6 S C=C[C@H](C....
35 1QIQ - ACC C13 H24 N3 O6 S2 CSC[C@H](C....
36 1BLZ - ACV C14 H25 N3 O6 S CC(C)[C@H]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: M9F; Similar ligands found: 24
No: Ligand ECFP6 Tc MDL keys Tc
1 M9F 1 1
2 ACV 0.758621 0.906977
3 M2W 0.698413 0.911111
4 W05 0.666667 0.904762
5 HFV 0.65625 0.791667
6 M8F 0.640625 0.866667
7 VB1 0.639344 0.883721
8 CDH 0.609375 0.808511
9 HCV 0.590909 0.906977
10 BCV 0.584615 0.840909
11 ASV 0.584615 0.840909
12 ACW 0.573529 0.791667
13 V10 0.565217 0.808511
14 V20 0.565217 0.808511
15 HCG 0.5625 0.860465
16 OCV 0.544118 0.782609
17 WT4 0.528571 0.886364
18 KKA 0.52459 0.833333
19 ACC 0.458333 0.888889
20 VAZ 0.454545 0.740741
21 M11 0.438356 0.73913
22 MDZ 0.438356 0.73913
23 GSH 0.405797 0.837209
24 SCV 0.4 0.744681
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1ODM; Ligand: ASV; Similar sites found: 177
This union binding pocket(no: 1) in the query (biounit: 1odm.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5BVS EIC 0.01209 0.40479 1.51515
2 5LY2 OGA 0.0004602 0.50122 1.81269
3 5FWE OGA 0.0006113 0.49399 1.81269
4 2YBP 2HG 0.001264 0.47831 1.81269
5 5F3I 5UJ 0.007009 0.42139 1.81269
6 2Y7P SAL 0.03348 0.40172 1.83486
7 5HV0 AKG 0.0001879 0.41818 1.84332
8 2XMY CDK 0.006074 0.42993 2.01342
9 4U0W 16G 0.01128 0.40278 2.03252
10 5M0T AKG 0.002468 0.46381 2.04082
11 2VFT SOR 0.0173 0.4084 2.1148
12 1OS7 AKG 0.008019 0.40287 2.12014
13 1OS7 TAU 0.008019 0.40287 2.12014
14 5EPA AKG 0.0006929 0.48965 2.15054
15 1SDW IYT 0.0195 0.40205 2.2293
16 4OCT AKG 0.00005515 0.53193 2.25225
17 3A6T 8OG 0.002784 0.43428 2.32558
18 4P7X YCP 0.003373 0.42649 2.39726
19 5FWJ MMK 0.003287 0.44915 2.41692
20 4RZB NFQ 0.007919 0.42976 2.41692
21 3KJM 245 0.007233 0.42296 2.41692
22 2RDQ AKG 0.002578 0.42072 2.43056
23 5T7I LAT NAG GAL 0.01365 0.42323 2.58065
24 5FQK 6NT 0.01583 0.42087 2.60223
25 5KBE IPH 0.01917 0.41448 2.62009
26 2PCU ASP 0.01209 0.4204 2.62295
27 1LNM DTX 0.009083 0.40052 2.71739
28 3OPT AKG 0.004114 0.45042 2.71903
29 3A16 PXO 0.01556 0.40042 2.71903
30 3ZJX BOG 0.02956 0.40357 2.76817
31 4XAC AKG 0.0003193 0.51036 2.77778
32 3AVR OGA 0.000064 0.5457 3.02115
33 3PUA OGA 0.0001771 0.52308 3.02115
34 5FP3 3JI 0.0009559 0.43527 3.02115
35 3AVS OGA 0.0002176 0.40231 3.02115
36 5J3Z 6FQ 0.02119 0.41133 3.125
37 5D3U TRP 0.0283 0.40558 3.32326
38 5W0N UPU 0.03301 0.40205 3.32326
39 2CM4 RCL 0.003881 0.41317 3.33333
40 4HIA FMN 0.005202 0.41094 3.40909
41 4OJ8 AKG 0.0005322 0.45388 3.41297
42 4OJ8 2TQ 0.00229 0.41949 3.41297
43 5EVY SAL 0.02604 0.41007 3.42466
44 5JSP DQY 0.02692 0.40762 3.48259
45 5NBW 8SK 0.01019 0.41574 3.6036
46 3KV5 OGA 0.0002274 0.52295 3.62538
47 4IE6 UN9 0.0003341 0.42975 3.62538
48 5FXD H7Y 0.006255 0.41804 3.62538
49 1I82 BGC BGC 0.03436 0.40309 3.7037
50 4IAW LIZ 0.005238 0.43417 3.7234
51 1U0A BGC BGC BGC BGC 0.007273 0.41502 3.73832
52 2Q8C AKG 0.0007651 0.48851 3.92749
53 2P5B OGA 0.00311 0.44068 3.92749
54 1OJJ GLC GAL 0.0101 0.42439 3.92749
55 5KR7 6X9 0.008237 0.42022 3.92749
56 1ULE GLA GAL NAG 0.0008407 0.4874 4
57 5I0U DCY 0.0002285 0.40581 4
58 5IQT AKG 0.004927 0.41205 4.12698
59 4MOB ADP 0.03586 0.40154 4.22961
60 3Q8G PEE 0.00237 0.44216 4.375
61 3KV4 OGA 0.0005926 0.49642 4.53172
62 5X7Q GLC GLC GLC GLC GLC 0.003304 0.45074 4.53172
63 5X7Q GLC GLC GLC GLC 0.003438 0.44528 4.53172
64 4Y3O OGA 0.005587 0.4427 5.13595
65 4CCO OGA 0.01191 0.4253 5.13595
66 4CCN OGA 0.009653 0.42478 5.13595
67 5MOB A8S 0.02459 0.40078 5.17241
68 4ZSI 4R1 0.004522 0.42455 5.26316
69 4ZSI GLP 0.009193 0.41031 5.26316
70 1N5S ADL 0.0001955 0.48746 5.35714
71 2JIG PD2 0.0000277 0.42827 5.35714
72 4QDF 30Q 0.01005 0.40851 5.43807
73 4HN1 TYD 0.01299 0.4146 5.47264
74 1OIK AKG 0.001282 0.47598 5.64784
75 1OIK C26 0.004241 0.42584 5.64784
76 4RFR RHN 0.001583 0.43727 5.91133
77 3KO0 TFP 0.02987 0.40363 5.94059
78 5L9B AKG 0.000006372 0.57823 5.95238
79 5L9V OGA 0.000007753 0.57402 5.95238
80 4BQY FNT 0.00002901 0.50852 5.95238
81 5ML3 DL3 0.006785 0.40834 6.04027
82 5KWY C3S 0.006545 0.41714 6.07287
83 3HQR OGA 0.00002046 0.54595 6.09756
84 1OW4 2AN 0.01589 0.40638 6.20155
85 1Y0G 8PP 0.01312 0.40112 6.28272
86 1QY1 PRZ 0.0001206 0.47711 6.32184
87 3PUR 2HG 0.00008406 0.542 6.34441
88 3N9O OGA 0.0002703 0.51726 6.34441
89 3N9Q OGA 0.0002873 0.51585 6.34441
90 2OVW CBI 0.03066 0.40375 6.34441
91 3QRC SCR 0.0001579 0.51939 6.36943
92 5AIG VPR 0.002254 0.4523 6.4
93 5OO5 UUA 0.003231 0.4313 6.45161
94 4QCK ASD 0.01342 0.40622 6.64653
95 3KFF XBT 0.00399 0.45009 6.79012
96 3KFF ZBT 0.00399 0.45009 6.79012
97 5HZX 2GE 0.0221 0.4031 6.81818
98 2YMZ LAT 0.0001163 0.55756 6.92308
99 4WOE ADP 0.02876 0.40542 6.94864
100 4Y24 TD2 0.001014 0.46945 7.14286
101 2IUW AKG 0.00004383 0.41955 7.14286
102 4FFG 0U8 0.03505 0.40067 7.25076
103 3MTX PGT 0.003836 0.41274 7.28477
104 3RGA LSB 0.01182 0.40526 7.42049
105 3WV6 GAL BGC 0.0001297 0.54947 7.43243
106 3WV6 GAL GLC 0.0003397 0.51497 7.43243
107 3HPY MCT 0.03364 0.40162 7.44337
108 2ET1 GLV 0.0009995 0.48367 7.46269
109 5V1B 8UY 0.00003851 0.5549 7.5
110 5BU3 4W9 0.006738 0.40299 7.6087
111 4WVW SLT 0.006356 0.44394 7.63889
112 4JZR 4JR 0.00002624 0.55545 7.87037
113 1W6O LAT 0.005507 0.44472 8.20895
114 1GZW GAL BGC 0.006169 0.44179 8.20895
115 1W6P NDG GAL 0.01315 0.42791 8.20895
116 2HKA C3S 0.007216 0.40813 8.46154
117 1EPB REA 0.001019 0.45442 8.53659
118 4N14 WR7 0.0137 0.40119 8.59873
119 4QM9 CYS 0.004296 0.45301 8.67052
120 5C5T AKG 0.000008087 0.58134 8.77193
121 5H9P TD2 0.006255 0.43991 8.86076
122 5L2J 70E 0.01454 0.41472 9.18367
123 5L2J 6UL 0.01365 0.41472 9.18367
124 2R5V HHH 0.00803 0.42076 9.36556
125 1DZK PRZ 0.006717 0.41661 9.55414
126 3SK2 GRI 0.01578 0.42071 9.84848
127 4CPB GAL CN8 0.02686 0.4028 9.91736
128 3H7J PPY 0.0005414 0.47205 9.96979
129 5E89 TD2 0.00379 0.4281 10.0719
130 1AUA BOG 0.009155 0.43128 10.1351
131 1C1L GAL BGC 0.001464 0.4755 10.219
132 1OGZ EQU 0.002066 0.44926 10.4
133 2YG2 S1P 0.0004301 0.44969 10.4651
134 2YG2 FLC 0.0005092 0.43342 10.4651
135 5U98 1KX 0.0195 0.4045 10.8303
136 5DG2 GAL GLC 0.0002287 0.52646 11.1111
137 5LXB 7A9 0.03054 0.40298 11.157
138 4M26 AKG 0.00005034 0.55394 11.1782
139 4M26 ZZU 0.001271 0.41743 11.1782
140 4M26 SIN 0.001271 0.41743 11.1782
141 3VQ2 LP4 LP5 MYR DAO 0.005819 0.4163 11.4804
142 5UQD AKG 0.0002889 0.51645 11.7825
143 3MPB FRU 0.007673 0.41772 12.0846
144 2ZHL NAG GAL GAL NAG 0.0004714 0.48022 12.1622
145 4XCB AKG 0.0004599 0.49891 12.2605
146 4XCB HY0 0.0006673 0.42927 12.2605
147 2AGC DAO 0.01861 0.41085 12.3457
148 5KEW 6SB 0.001609 0.47204 12.5
149 2HZQ STR 0.01438 0.42305 12.6437
150 2WA4 069 0.000165 0.50221 12.9909
151 4B7E OGA 0.0008003 0.48813 12.9909
152 3P3N AKG 0.0006864 0.48594 12.9909
153 2XUM OGA 0.0007752 0.4859 12.9909
154 1H2M OGA 0.0008571 0.48338 12.9909
155 1H2K OGA 0.0008937 0.48242 12.9909
156 2Y0I AKG 0.001127 0.47912 12.9909
157 4L4J NAG NAG BMA MAN NAG 0.0006516 0.50037 13.1222
158 1WUB OTP 0.001194 0.44577 14.0449
159 3WG3 A2G GAL NAG FUC 0.0006513 0.4848 14.6067
160 1LFO OLA 0.005308 0.41404 14.8438
161 4J25 OGA 0.00002877 0.56404 15.7205
162 4REI 3MV 0.01807 0.41587 15.894
163 1WW5 SGA BGC 0.006105 0.44241 16.25
164 5H9Q TD2 0.0002178 0.52472 16.7742
165 4RLT FSE 0.02015 0.40136 17.6871
166 4GJY OGA 0.00238 0.45783 17.8723
167 3G08 FEE 0.001217 0.4549 18.1818
168 1UNB AKG 0.0000001388 0.55215 20.5788
169 1UNB PN1 0.0000001311 0.53617 20.5788
170 5LUN OGA 0.0000554 0.54669 25.6798
171 5LUN ARG 0.0002768 0.44418 25.6798
172 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.00005772 0.50077 31.8584
173 1GP6 QUE 0.00001508 0.50248 37.1601
174 1GP6 DH2 0.00001816 0.49716 37.1601
175 1GP6 SIN 0.00001816 0.49716 37.1601
176 5C3R HMU 0.00000122 0.58171 44.4109
177 5C3R AKG 0.00000122 0.58171 44.4109
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