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
38.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.76, H-bond role recall 0.55
Reason: no major geometry red flags detected
1 protein-contact clashes
42% of hydrophobic surface appears solvent-exposed (11/26 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 (-0.904 kcal/mol/HA)
✓ Good fit quality (FQ -9.12)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Very high strain energy (38.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-31.652
kcal/mol
LE
-0.904
kcal/mol/HA
Fit Quality
-9.12
FQ (Leeson)
HAC
35
heavy atoms
MW
503
Da
LogP
2.03
cLogP
Interaction summary
HB 8
HY 13
PI 0
CLASH 1
⚠ Exposure 42%
Interaction summary
HB 8
HY 13
PI 0
CLASH 1
⚠ Exposure 42%
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
Partial hydrophobic solvent exposure
42% of hydrophobic surface appears solvent-exposed (11/26 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 26
Buried (contacted) 15
Exposed 11
LogP 2.03
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 5.153 | Score | -31.652 |
|---|---|---|---|
| Inter norm | -0.894 | Intra norm | -0.010 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 8 |
| Artifact reason | geometry warning; 17 clashes; 3 protein clashes; high strain Δ 38.1 | ||
| Residues |
ALA24
ALA40
ASN41
ASP129
GLU21
GLU73
GLY23
GLY25
LEU130
LYS127
LYS159
LYS26
PHE38
SER22
SER27
SER28
| ||
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 | 0.76 | 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 |
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 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 280 | 3.072939621275057 | -0.652326 | -26.0627 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 262 | 4.357606610843862 | -0.719793 | -20.2471 | 13 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 352 | 4.377816770020476 | -0.688479 | -23.3913 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 299 | 4.8568129299279565 | -0.590291 | -13.2375 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 221 | 5.152576031245613 | -0.894038 | -31.6518 | 8 | 16 | 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
-31.652kcal/mol
Ligand efficiency (LE)
-0.9043kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.122
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
502.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.03
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
96.21kcal/mol
Minimised FF energy
58.06kcal/mol
SASA & burial
✓ computed
SASA (unbound)
786.1Ų
Total solvent-accessible surface area of free ligand
BSA total
537.9Ų
Buried surface area upon binding
BSA apolar
438.6Ų
Hydrophobic contacts buried
BSA polar
99.3Ų
Polar contacts buried
Fraction buried
68.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1514.3Ų
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
527.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)