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 mixed
SASA done
Strain ΔE
38.8 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.52, Jaccard 0.38, H-bond role recall 0.36
Reason: 9 protein-contact clashes, 9 internal clashes
9 protein-contact clashes
9 intramolecular clashes
58% of hydrophobic surface appears solvent-exposed (7/12 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 (-1.305 kcal/mol/HA)
✓ Good fit quality (FQ -11.51)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ Very high strain energy (38.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-30.006
kcal/mol
LE
-1.305
kcal/mol/HA
Fit Quality
-11.51
FQ (Leeson)
HAC
23
heavy atoms
MW
339
Da
LogP
-0.18
cLogP
Interaction summary
HB 16
HY 2
PI 0
CLASH 9
⚠ Exposure 58%
Interaction summary
HB 16
HY 2
PI 0
CLASH 9
⚠ Exposure 58%
Partial hydrophobic solvent exposure
58% of hydrophobic surface appears solvent-exposed (7/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 12
Buried (contacted) 5
Exposed 7
LogP -0.18
H-bonds 16
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 4.737 | Score | -30.006 |
|---|---|---|---|
| Inter norm | -1.374 | Intra norm | 0.070 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 16 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes; high strain Δ 38.8 | ||
| Residues |
ALA24
ALA70
ASP68
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
ILE46
LYS127
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.38 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 314 | 0.5830381536909487 | -1.04181 | -23.0673 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 333 | 0.9733101179093773 | -0.908412 | -18.6961 | 7 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 311 | 1.3217602217415956 | -0.91107 | -18.479 | 8 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 315 | 2.5490921636830532 | -1.06419 | -25.9922 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 399 | 2.564496477601504 | -1.01598 | -21.549 | 10 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 282 | 4.379667419655693 | -1.40933 | -26.968 | 16 | 20 | 13 | 0.62 | 0.18 | - | no | Open |
| 300 | 4.737160626904453 | -1.37439 | -30.006 | 16 | 19 | 11 | 0.52 | 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
-30.006kcal/mol
Ligand efficiency (LE)
-1.3046kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.514
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
339.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.18
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-58.53kcal/mol
Minimised FF energy
-97.30kcal/mol
SASA & burial
✓ computed
SASA (unbound)
544.2Ų
Total solvent-accessible surface area of free ligand
BSA total
481.1Ų
Buried surface area upon binding
BSA apolar
302.4Ų
Hydrophobic contacts buried
BSA polar
178.7Ų
Polar contacts buried
Fraction buried
88.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1206.8Ų
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
510.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)