Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
28.8 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.71, Jaccard 0.62, H-bond role recall 0.45
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
64% of hydrophobic surface is solvent-exposed (18/28 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. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.880 kcal/mol/HA)
✓ Good fit quality (FQ -9.14)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (28.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-34.339
kcal/mol
LE
-0.880
kcal/mol/HA
Fit Quality
-9.14
FQ (Leeson)
HAC
39
heavy atoms
MW
563
Da
LogP
5.00
cLogP
Final rank
4.6552
rank score
Inter norm
-0.829
normalised
Contacts
18
H-bonds 10
Interaction summary
HBD 1
HBA 6
HY 2
PI 0
CLASH 5
Interaction summary
HBD 1
HBA 6
HY 2
PI 0
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 15 | Native recall | 0.71 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 475 | 1.280287287729594 | -0.617165 | -25.0747 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 463 | 2.6296067961054295 | -0.682535 | -26.5323 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 514 | 3.7948270720513495 | -0.709367 | -28.2621 | 7 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 473 | 4.655184917891928 | -0.82917 | -34.339 | 10 | 18 | 15 | 0.71 | 0.45 | - | no | Current |
| 457 | 5.557439725654371 | -0.634517 | -20.1581 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 460 | 5.792579168189608 | -0.711207 | -22.3926 | 8 | 22 | 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
-34.339kcal/mol
Ligand efficiency (LE)
-0.8805kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.138
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
563.1Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.00
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
114.31kcal/mol
Minimised FF energy
85.51kcal/mol
SASA & burial
✓ computed
SASA (unbound)
858.3Ų
Total solvent-accessible surface area of free ligand
BSA total
577.9Ų
Buried surface area upon binding
BSA apolar
471.6Ų
Hydrophobic contacts buried
BSA polar
106.3Ų
Polar contacts buried
Fraction buried
67.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1538.1Ų
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
559.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)