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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
20.6 kcal/mol
Protein clashes
0
Internal clashes
7
Native overlap
contact recall 0.90, Jaccard 0.83, H-bond role recall 0.45
Reason: 7 internal clashes
7 intramolecular clashes
57% of hydrophobic surface appears solvent-exposed (8/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.491 kcal/mol/HA)
✓ Good fit quality (FQ -13.16)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ High strain energy (20.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-34.294
kcal/mol
LE
-1.491
kcal/mol/HA
Fit Quality
-13.16
FQ (Leeson)
HAC
23
heavy atoms
MW
375
Da
LogP
1.81
cLogP
Final rank
3.9368
rank score
Inter norm
-1.633
normalised
Contacts
21
H-bonds 11
Interaction summary
HBD 1
HBA 7
HY 2
PI 1
CLASH 0
Interaction summary
HBD 1
HBA 7
HY 2
PI 1
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
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 | 19 | Native recall | 0.90 |
| Jaccard | 0.83 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 361 | 2.928981575060389 | -1.18606 | -26.5253 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 462 | 3.5611515835005716 | -1.07153 | -23.9906 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 338 | 3.9315534075534533 | -1.1776 | -25.6128 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 361 | 3.9368268407414826 | -1.63301 | -34.2943 | 11 | 21 | 19 | 0.90 | 0.45 | - | no | Current |
| 386 | 4.140880293503326 | -1.19197 | -25.8274 | 11 | 17 | 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
-34.294kcal/mol
Ligand efficiency (LE)
-1.4911kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.160
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
374.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.81
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-131.91kcal/mol
Minimised FF energy
-152.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
566.9Ų
Total solvent-accessible surface area of free ligand
BSA total
497.4Ų
Buried surface area upon binding
BSA apolar
341.9Ų
Hydrophobic contacts buried
BSA polar
155.5Ų
Polar contacts buried
Fraction buried
87.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1266.1Ų
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
497.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)