Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
13.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.52, Jaccard 0.42, H-bond role recall 0.27
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
50% of hydrophobic surface appears solvent-exposed (7/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.612 kcal/mol/HA)
✓ Good fit quality (FQ -12.92)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (13.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-29.020
kcal/mol
LE
-1.612
kcal/mol/HA
Fit Quality
-12.92
FQ (Leeson)
HAC
18
heavy atoms
MW
240
Da
LogP
2.50
cLogP
Interaction summary
HB 9
HY 5
PI 0
CLASH 4
⚠ Exposure 50%
Interaction summary
HB 9
HY 5
PI 0
CLASH 4
⚠ Exposure 50%
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (7/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 14
Buried (contacted) 7
Exposed 7
LogP 2.5
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.251 | Score | -29.020 |
|---|---|---|---|
| Inter norm | -1.764 | Intra norm | 0.152 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 9 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes | ||
| Residues |
ALA24
GLN42
GLU21
GLU73
GLY23
GLY25
GLY47
GLY71
LEU31
LEU39
LYS26
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 | 0.42 | RMSD | - |
| HB strict | 4 | Strict recall | 0.27 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 3 | HB residue recall | 0.27 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 278 | -0.8574207073241159 | -1.70687 | -28.9721 | 8 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 266 | 1.5959075923798347 | -1.34226 | -22.3319 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 213 | 1.7738857891499675 | -1.54371 | -24.8335 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 318 | 3.068718716092686 | -1.39908 | -21.0296 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 242 | 3.2507870146011015 | -1.76408 | -29.0198 | 9 | 16 | 11 | 0.52 | 0.27 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.020kcal/mol
Ligand efficiency (LE)
-1.6122kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.921
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
240.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.50
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
35.52kcal/mol
Minimised FF energy
22.23kcal/mol
SASA & burial
✓ computed
SASA (unbound)
457.1Ų
Total solvent-accessible surface area of free ligand
BSA total
428.0Ų
Buried surface area upon binding
BSA apolar
350.0Ų
Hydrophobic contacts buried
BSA polar
78.0Ų
Polar contacts buried
Fraction buried
93.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1245.2Ų
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
499.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)