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
3
Internal clashes
3
Native overlap
contact recall 0.86, Jaccard 0.62, H-bond role recall 0.09
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
60% of hydrophobic surface is solvent-exposed (15/25 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Risk
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.917 kcal/mol/HA)
✓ Good fit quality (FQ -8.85)
✓ Good H-bonds (4 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ Moderate strain (16.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-27.507
kcal/mol
LE
-0.917
kcal/mol/HA
Fit Quality
-8.85
FQ (Leeson)
HAC
30
heavy atoms
MW
403
Da
LogP
4.31
cLogP
Final rank
2.2079
rank score
Inter norm
-1.037
normalised
Contacts
26
H-bonds 7
Interaction summary
HBD 3
HBA 1
HY 5
PI 1
CLASH 3
Interaction summary
HBD 3
HBA 1
HY 5
PI 1
CLASH 3
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 | 18 | Native recall | 0.86 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 1 | Strict recall | 0.07 |
| HB same residue+role | 1 | HB role recall | 0.09 |
| HB same residue | 2 | HB residue recall | 0.18 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 161 | 2.2078640336338715 | -1.03668 | -27.5069 | 7 | 26 | 18 | 0.86 | 0.09 | - | no | Current |
| 204 | 4.4614773907661345 | -0.794682 | -21.3519 | 5 | 20 | 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
-27.507kcal/mol
Ligand efficiency (LE)
-0.9169kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.845
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
402.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.31
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
73.20kcal/mol
Minimised FF energy
56.31kcal/mol
SASA & burial
✓ computed
SASA (unbound)
753.0Ų
Total solvent-accessible surface area of free ligand
BSA total
689.4Ų
Buried surface area upon binding
BSA apolar
640.0Ų
Hydrophobic contacts buried
BSA polar
49.4Ų
Polar contacts buried
Fraction buried
91.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
92.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1574.1Ų
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
496.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)