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
32.4 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.86, Jaccard 0.82, H-bond role recall 0.45
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
54% of hydrophobic surface appears solvent-exposed (7/13 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 (-1.327 kcal/mol/HA)
✓ Good fit quality (FQ -11.71)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Very high strain energy (32.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-30.522
kcal/mol
LE
-1.327
kcal/mol/HA
Fit Quality
-11.71
FQ (Leeson)
HAC
23
heavy atoms
MW
440
Da
LogP
2.69
cLogP
Interaction summary
HB 9
HY 4
PI 1
CLASH 4
⚠ Exposure 53%
Interaction summary
HB 9
HY 4
PI 1
CLASH 4
⚠ Exposure 53%
Partial hydrophobic solvent exposure
54% of hydrophobic surface appears solvent-exposed (7/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 13
Buried (contacted) 6
Exposed 7
LogP 2.69
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.265 | Score | -30.522 |
|---|---|---|---|
| Inter norm | -1.480 | Intra norm | 0.153 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 9 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes; high strain Δ 32.4 | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLU73
GLY23
GLY25
LEU130
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
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 | 18 | Native recall | 0.86 |
| Jaccard | 0.82 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 547 | 0.0001686980135924207 | -1.31119 | -26.8288 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 561 | 0.7491426789319044 | -1.12946 | -21.5955 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 543 | 0.8581889703670903 | -1.10564 | -21.5184 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 581 | 2.532328841747823 | -1.16313 | -22.5779 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 583 | 2.5350167377201838 | -0.924274 | -20.1771 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 555 | 3.2652800986751 | -1.28367 | -26.9365 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 569 | 3.2652825576278226 | -1.47996 | -30.5218 | 9 | 19 | 18 | 0.86 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.522kcal/mol
Ligand efficiency (LE)
-1.3270kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.712
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
439.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.69
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-75.58kcal/mol
Minimised FF energy
-107.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
576.5Ų
Total solvent-accessible surface area of free ligand
BSA total
467.3Ų
Buried surface area upon binding
BSA apolar
342.6Ų
Hydrophobic contacts buried
BSA polar
124.8Ų
Polar contacts buried
Fraction buried
81.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1254.5Ų
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
529.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)