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
23.3 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.71, Jaccard 0.52, H-bond role recall 0.36
Reason: 9 protein-contact clashes, 9 internal clashes
9 protein-contact clashes
9 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.014 kcal/mol/HA)
✓ Good fit quality (FQ -9.88)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (23.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-31.424
kcal/mol
LE
-1.014
kcal/mol/HA
Fit Quality
-9.88
FQ (Leeson)
HAC
31
heavy atoms
MW
442
Da
LogP
0.80
cLogP
Interaction summary
HB 13
HY 5
PI 0
CLASH 9
Interaction summary
HB 13
HY 5
PI 0
CLASH 9
| Final rank | 4.493 | Score | -31.424 |
|---|---|---|---|
| Inter norm | -1.037 | Intra norm | 0.023 |
| Top1000 | no | Excluded | no |
| Contacts | 23 | H-bonds | 13 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 23.0 | ||
| Residues |
ALA24
ALA40
ALA70
ASN41
ASP68
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
ILE46
LEU130
LYS127
LYS159
LYS26
PHE38
SER22
SER27
SER28
THR44
THR69
| ||
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 | ||
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 | 0.52 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 355 | 1.6026500140535416 | -0.743905 | -21.8571 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 354 | 1.7306580484949365 | -0.923116 | -29.7352 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 407 | 2.0338986117039672 | -0.876746 | -27.1056 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 358 | 2.1591494369409356 | -0.901399 | -28.0656 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 3.080838426070046 | -0.679833 | -20.0918 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 357 | 4.492732902768604 | -1.03651 | -31.4245 | 13 | 23 | 15 | 0.71 | 0.36 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.424kcal/mol
Ligand efficiency (LE)
-1.0137kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.876
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
442.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.80
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
19.63kcal/mol
Minimised FF energy
-3.70kcal/mol
SASA & burial
✓ computed
SASA (unbound)
704.6Ų
Total solvent-accessible surface area of free ligand
BSA total
624.0Ų
Buried surface area upon binding
BSA apolar
461.1Ų
Hydrophobic contacts buried
BSA polar
162.9Ų
Polar contacts buried
Fraction buried
88.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1381.5Ų
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
499.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)