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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
15.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.70, H-bond role recall 0.36
Reason: no major geometry red flags detected
1 protein-contact clashes
64% of hydrophobic surface is solvent-exposed (14/22 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.927 kcal/mol/HA)
✓ Good fit quality (FQ -8.75)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ Moderate strain (15.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-25.959
kcal/mol
LE
-0.927
kcal/mol/HA
Fit Quality
-8.75
FQ (Leeson)
HAC
28
heavy atoms
MW
369
Da
LogP
2.86
cLogP
Interaction summary
HB 7
HY 4
PI 1
CLASH 1
⚠ Exposure 63%
Interaction summary
HB 7
HY 4
PI 1
CLASH 1
⚠ Exposure 63%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
64% of hydrophobic surface is solvent-exposed (14/22 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 22
Buried (contacted) 8
Exposed 14
LogP 2.86
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 2.808 | Score | -25.959 |
|---|---|---|---|
| Inter norm | -1.104 | Intra norm | 0.177 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 7 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU43
GLY23
GLY25
LEU130
LYS127
LYS159
LYS26
PHE38
SER157
SER27
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 39 | 0.2926143135980963 | -1.11467 | -31.7234 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 69 | 0.9875579684309523 | -0.781677 | -18.8622 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 37 | 1.026816980381705 | -0.901056 | -26.2142 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 66 | 1.5219351344448833 | -1.19323 | -33.0077 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 64 | 2.068825905927844 | -0.72591 | -19.4561 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 35 | 2.8077876146014913 | -1.10435 | -25.9593 | 7 | 18 | 16 | 0.76 | 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
-25.959kcal/mol
Ligand efficiency (LE)
-0.9271kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.752
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
369.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.86
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
32.25kcal/mol
Minimised FF energy
16.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
669.1Ų
Total solvent-accessible surface area of free ligand
BSA total
568.1Ų
Buried surface area upon binding
BSA apolar
482.7Ų
Hydrophobic contacts buried
BSA polar
85.4Ų
Polar contacts buried
Fraction buried
84.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1408.5Ų
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
527.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)