Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
16.9 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.95, Jaccard 0.80, H-bond role recall 0.45
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
44% of hydrophobic surface appears solvent-exposed (8/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.103 kcal/mol/HA)
✓ Good fit quality (FQ -10.16)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Moderate strain (16.9 kcal/mol)
✗ Geometry warnings
Score
-28.677
kcal/mol
LE
-1.103
kcal/mol/HA
Fit Quality
-10.16
FQ (Leeson)
HAC
26
heavy atoms
MW
350
Da
LogP
2.45
cLogP
Final rank
2.9638
rank score
Inter norm
-1.241
normalised
Contacts
24
H-bonds 16
Interaction summary
HBA 7
HY 3
PI 1
CLASH 5
Interaction summary
HBA 7
HY 3
PI 1
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 20 | Native recall | 0.95 |
| Jaccard | 0.80 | RMSD | - |
| HB strict | 8 | Strict recall | 0.53 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 232 | 0.22512664578509115 | -0.982056 | -23.3495 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 203 | 0.6142823023382752 | -1.00213 | -23.6948 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 285 | 1.1222800013457437 | -0.984396 | -22.608 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 238 | 1.9179388927226144 | -1.20382 | -29.2649 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 234 | 2.1949120016563737 | -1.18622 | -28.0822 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 341 | 2.442548170009624 | -0.972273 | -22.0173 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 213 | 2.9637696841486436 | -1.24057 | -28.6769 | 16 | 24 | 20 | 0.95 | 0.45 | - | no | Current |
| 167 | 3.258232707517787 | -1.05416 | -24.6519 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.677kcal/mol
Ligand efficiency (LE)
-1.1030kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.162
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
350.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.45
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.71kcal/mol
Minimised FF energy
25.76kcal/mol
SASA & burial
✓ computed
SASA (unbound)
637.0Ų
Total solvent-accessible surface area of free ligand
BSA total
568.2Ų
Buried surface area upon binding
BSA apolar
490.8Ų
Hydrophobic contacts buried
BSA polar
77.4Ų
Polar contacts buried
Fraction buried
89.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1420.0Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
503.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)