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
36.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.55
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.803 kcal/mol/HA)
✓ Good fit quality (FQ -15.91)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Very high strain energy (36.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-41.476
kcal/mol
LE
-1.803
kcal/mol/HA
Fit Quality
-15.91
FQ (Leeson)
HAC
23
heavy atoms
MW
331
Da
LogP
2.93
cLogP
Interaction summary
HB 11
HY 3
PI 1
CLASH 4
Interaction summary
HB 11
HY 3
PI 1
CLASH 4
| Final rank | 4.127 | Score | -41.476 |
|---|---|---|---|
| Inter norm | -1.490 | Intra norm | -0.313 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 11 |
| Artifact reason | geometry warning; 9 clashes; 3 protein clashes; high strain Δ 36.1 | ||
| Residues |
ALA158
ALA24
ASN126
ASP129
GLU73
GLY23
GLY25
GLY71
LEU130
LYS127
LYS159
LYS26
PHE38
SER157
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 6 | HB residue recall | 0.55 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 533 | 0.05601415744938339 | -1.35636 | -41.8697 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 524 | 4.127316334406169 | -1.49003 | -41.4757 | 11 | 19 | 16 | 0.76 | 0.55 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-41.476kcal/mol
Ligand efficiency (LE)
-1.8033kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-15.915
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
331.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.93
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
95.23kcal/mol
Minimised FF energy
59.16kcal/mol
SASA & burial
✓ computed
SASA (unbound)
573.1Ų
Total solvent-accessible surface area of free ligand
BSA total
509.2Ų
Buried surface area upon binding
BSA apolar
336.1Ų
Hydrophobic contacts buried
BSA polar
173.2Ų
Polar contacts buried
Fraction buried
88.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1260.9Ų
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
493.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)