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 high
Native strong
SASA done
Strain ΔE
15.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.95, H-bond role recall 0.45
Reason: no major geometry red flags detected
1 protein-contact clashes
41% of hydrophobic surface appears solvent-exposed (7/17 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 (-1.505 kcal/mol/HA)
✓ Good fit quality (FQ -13.68)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Moderate strain (15.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-37.614
kcal/mol
LE
-1.505
kcal/mol/HA
Fit Quality
-13.68
FQ (Leeson)
HAC
25
heavy atoms
MW
358
Da
LogP
1.37
cLogP
Interaction summary
HB 12
HY 9
PI 1
CLASH 1
⚠ Exposure 41%
Interaction summary
HB 12
HY 9
PI 1
CLASH 1
⚠ Exposure 41%
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
Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 10
Exposed 7
LogP 1.37
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 4.697 | Score | -37.614 |
|---|---|---|---|
| Inter norm | -1.496 | Intra norm | -0.009 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 12 |
| Artifact reason | geometry warning; 11 clashes; 4 protein clashes | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
THR44
| ||
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 | 21 | Native recall | 1.00 |
| Jaccard | 0.95 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 486 | 1.9052161049866707 | -1.31228 | -33.2714 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 492 | 3.034214712574297 | -1.15728 | -28.8737 | 14 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 533 | 3.449464694652645 | -0.899623 | -24.2548 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 509 | 4.697174026972678 | -1.49588 | -37.6138 | 12 | 22 | 21 | 1.00 | 0.45 | - | no | Current |
| 521 | 5.217968059341253 | -0.989094 | -25.0463 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-37.614kcal/mol
Ligand efficiency (LE)
-1.5046kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.678
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
358.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.37
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-80.22kcal/mol
Minimised FF energy
-96.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
586.0Ų
Total solvent-accessible surface area of free ligand
BSA total
524.9Ų
Buried surface area upon binding
BSA apolar
377.2Ų
Hydrophobic contacts buried
BSA polar
147.7Ų
Polar contacts buried
Fraction buried
89.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1268.3Ų
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
502.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)